Oligonucleotide compositions and methods of making the same

ABSTRACT

The present disclosure provides a solid phase method of making oligonucleotides via sequential coupling cycles including at least one coupling of a dinucleotide dimer subunit to a free 3′-terminal group of a growing chain. The oligonucleotides include at least two nucleoside subunits joined by a N3′→P5′ phosphoramidate linkage. The method may include the steps of (a) deprotecting the protected 3′ amino group of a terminal nucleoside attached to a solid phase support, said deprotecting forming a free 3′ amino group; (b) contacting the free 3′ amino group with a 3′-protected amino-dinucleotide-5′-phosphoramidite dimer in the presence of a nucleophilic catalyst to form an internucleoside N3′→P5′ phosphoramidite linkage; and (c) oxidizing (e.g., sulfurizing) the linkage. The compositions produced by the subject methods may include a reduced amount of one or more (N−x) oligonucleotide products. Also provided are pharmaceutical compositions including the subject oligonucleotide compositions.

CROSS REFERENCE TO RELATED APPLICATIONS

Pursuant to 35 U.S.C. § 119(e), this application claims priority to thefiling dates of U.S. provisional application Ser. No. 61/987,396, filedMay 1, 2014, and U.S. provisional application Ser. No. 62/151,909 filedApr. 23, 2015 (attorney reference number 185/002X), the disclosures ofwhich are herein incorporated by reference.

INTRODUCTION

Nucleic acid polymer chemistry has played a role in many developingtechnologies in the pharmaceutical, diagnostic, and analytical fields,and more particularly in the subfields of antisense and anti-genetherapeutics, combinatorial chemistry, branched DNA signalamplification, and array-based DNA diagnostics and analysis. Some ofthis polymer chemistry has been directed to improving the bindingstrength, specificity, and nuclease resistance of natural nucleic acidpolymers, such as DNA. Peptide nucleic acid (PNAs), phosphorothioate,methylphosphonate and phosphoramidate intemucleoside linkages areexamples of some polymer chemistries that have been applied tooligonucleotides to provide for one or more desirable properties such asnuclease resistance, cellular uptake and solubility.

Oligonucleotide N3′→P5′ phosphoramidates can form stable duplexes withcomplementary DNA and RNA strands, as well as stable triplexes with DNAduplexes, and are resistant to nucleases. Oligonucleotide N3′→P5′thiophosphoramidates have found use as potent antisense agents both invitro and in vivo. For example, oligonucleotide containing compoundsthat inhibit telomerase activity can be used to treattelomerase-mediated disorders, such as cancer, since cancer cellsexpress telomerase activity and normal human somatic cells do notpossess telomerase activity at biologically relevant levels. As such,methods of preparing and isolating such oligonucleotides are ofinterest.

SUMMARY

The present disclosure provides a solid phase method of makingoligonucleotides via sequential coupling cycles including at least onecoupling of a dinucleotide dimer subunit to a free 3′-terminal group(e.g., a 3′-hydroxyl or 3′-amino group) of a growing chain. The subjectmethods include making oligonucleotides where at least two of thenucleoside subunits are joined by a N3′→P5′ phosphoramidateinter-subunit linkage. The method may include the steps of (a)deprotecting the protected 3′ amino group of a terminal nucleosideattached to a solid phase support, said deprotecting forming a free 3′amino group; (b) contacting the free 3′ amino group with a 3′-protectedamino-dinucleotide-5′-phosphoramidite dimer in the presence of anucleophilic catalyst to form an internucleoside N3′→P5′ phosphoramiditelinkage; and (c) oxidizing the linkage. In some cases, oxidizing thelinkage include sulfurizing to produce an internucleoside N3′→P5′thiophosphoramidate linkage.

Aspects of the present disclosure include oligonucleotide compositionsproduced by the subject methods that include a reduced amount of one ormore (N−x) oligonucleotide products. In some cases, the reduced amountis less than (1.9×N) parts to 100 by weight of one or more (N−x)products relative to N product. Oligonucleotides prepared according tothe subject methods include an oligonucleotide having a sequence of Nnucleoside subunits complementary to the RNA component of humantelomerase, wherein at least two of the nucleoside subunits are joinedby a N3′→P5′ thiophosphoramidate inter-subunit linkage. Also providedare pharmaceutical compositions including the subject oligonucleotidecompositions.

BRIEF DESCRIPTION OF THE DRAWINGS

FIGS. 1A and 1B show an HPLC chromatogram (A) and ³¹P NMR spectra (B)for a TA dimer thiophosphoramidate (compound 7e, Scheme 1).

FIGS. 2A and 2B show an HPLC chromatogram (A) and ³¹P NMR spectra (B)for a AA dimer thiophosphoramidate (compound 7a, Scheme 1).

FIGS. 3A and 3B show an HPLC chromatogram (A) and ³¹P NMR spectra (B)for a GG dimer thiophosphoramidate (compound 7c, Scheme 1).

FIGS. 4A and 4B show an HPLC chromatogram (A) and ³¹P NMR spectra (B)for a GT dimer thiophosphoramidate (compound 7d, Scheme 1).

FIGS. 5A and 5B show an HPLC chromatogram (A) and ³¹P NMR spectra (B)for a GA dimer thiophosphoramidate (compound 7b, Scheme 1).

FIGS. 6A and 6B show LCMS traces for dimer amidates TA, AA, GA, GT andGG.

FIG. 7 shows an HPLC chromatogram of the product of a 140 μmole scalesynthesis of imetelstat using a monomer coupling strategy.

FIG. 8 shows an HPLC chromatogram of the product of a 140 μmole scalesynthesis of imetelstat using a dimer block coupling strategy.

DEFINITIONS

The following terms have the following meanings unless otherwiseindicated. Any undefined terms have their art recognized meanings.

As used herein, the terms polynucleotide and oligonucleotide are usedinterchangeably. Whenever an oligonucleotide is represented by asequence of letters, such as “ATGUCCTG,” it is understood that thenucleotides are in 5′→+3 order from left to right and that “A” denotesdeoxyadenosine. “C” denotes deoxycytidine, “G” denotes deoxyguanosine,“T” denotes thymidine, and “U” denotes deoxyuridine, unless otherwisenoted.

As used herein, “nucleoside” includes the natural nucleosides, including2′-deoxy and 2′-hydroxyl forms, e.g. as described in Kornberg and Baker,DNA Replication, 2nd Ed. (Freeman, San Francisco, 1992). “Analogs” inreference to nucleosides includes synthetic nucleosides having modifiedbase moieties and/or modified sugar moieties, e.g. described generallyby Scheit, Nucleotide Analogs (John Wiley, New York, 1980). Such analogsinclude synthetic nucleosides designed to enhance binding properties,e.g. stability, specificity, or the like, such as disclosed by Uhlmannand Peyman (Chemical Reviews, 90:543-584, 1990). In some embodiments, anucleoside or nucleoside analog includes a 3′-hydroxyl group or a3′-amino group.

The terms “base” and “nucleobase” are used interchangeably and definedherein to include (i) conventional DNA and RNA bases (uracil, thymine,adenine, guanine, and cytosine), and (ii) modified bases or base analogs(e.g., 5-methyl-cytosine, 5-bromouracil, or inosine). A base analog is achemical whose molecular structure mimics that of a conventional DNA orRNA base.

As used herein, “pyrimidine” means the pyrimidines occurring in naturalnucleosides, including cytosine, thymine, and uracil, and common analogsthereof, such as those containing oxy, methyl, propynyl, methoxy,hydroxyl, amino, thio, halo, and like, substituents. The term as usedherein further includes pyrimidines with common protection groupsattached, such as N4-benzoylcytosine. Further common pyrimidineprotection groups are disclosed by Beaucage and Iyer Tetrahedron 48:2223-2311 (1992).

As used herein, “purine” means the purines occurring in naturalnucleosides, including adenine, guanine, and hypoxanthine, and commonanalogs thereof, such as those containing oxy, methyl, propynyl,methoxy, hydroxyl, amino, thio, halo, and like, substituents. The termas used herein further includes purines with common protection groupsattached, such as N²-benzoylguanine, N²-isobutyrylguanine,N⁶-benzoyladenine, and the like. Further common purine protection groupsare disclosed by Beaucage and Iyer Tetrahedron 48: 2223-2311 (1992). Asused herein, the term “-protected-” as a component of a chemical namerefers to art-recognized protection groups for a particular moiety of acompound, e.g. “5′-protected-hydroxyl” in reference to a nucleosideincludes triphenylmethyl (i.e., trityl), p-anisyldiphenylmethyl (i.e.,monomethoxytrityl or MMT), di-p-anisylphenylmethyl (i.e.,dimethoxytrityl or DMT), and the like; and a protected nucleobase inreference to a nucleobase including a heteroatom protected with a groupsuch as a dimethylaminoformamidine (DMF), benzoyl (Bz), isobutyryl, andthe like. Art-recognized protection groups include those described inthe following references: Gait, editor, Oligonucleotide Synthesis: APractical Approach (IRL Press, Oxford, 1984); Amarnath and Broom,Chemical Reviews, 77:183-217, 1977; Pon et al., Biotechniques,6:768-775, 1988; Ohtsuka et al, Nicleic Acids Research, 10:6553-6570,1982; Eckstein, editor, Oligonucleotides. and Analogues: A PracticalApproach (IRL Press, Oxford, 1991), Greene and Wuts, Protective Groupsin Organic Synthesis, Second Edition, (John Wiley & Sons, New York,1991), Narang, editor, Synthesis and Applications of DNA and RNA(Academic Press, New York, 1987), Beaucage and Iyer Tetrahedron 48:2223-2311 (1992), and like references.

As used herein, “oligonucleotide N3′→P5′ phosphoramidate” means anoligomer, usually linear, of nucleoside subunits linked by at least oneN3′→P5′ phosphoramidate linkage. In general terms, the nucleosidesubunits comprise nucleosides or nucleoside analogs, but may alsocomprise more general moieties having compatible chemistry, such asabasic sugars and other hydrocarbon moieties, such as described in thefollowing references: Newton et al., Nucleic Acids Research, 21:1155-1162 (1993); Griffin et al, J. Am. Chem. Soc., 114: 7976-7982(1992); Jaschke et al, Tetrahedron Letters, 34: 301-304 (1992); Ma etal., International application PCT/CA92/00423; Zon et al., Internationalapplication PCT/US90/06630; Durand et al., Nucleic Acids Research, 18:6353-6359 (1990); Salunkhe et al., J. Am. Chem. Soc., 114: 8768-8772(1992); and the like. In some instances, the term means anoligonucleotide wherein all internucleosidic linkages are replaced byN3′→P5′ phosphoramidate linkages, i.e. the term comprehends partially aswell as fully “amidated” oligomers. In some instances, it means anoligonucleotide wherein all the internucleosidic linkages are replacedby N3′→P5′ phosphoramidate linkages and wherein the nucleoside subunitsare the natural nucleosides or analogs thereof. A subjectoligonucleotide N3′→P5′ phosphoramidate in which every linkage is anN3′→P5′ phosphoramidate linkage (“fully amidated”) may be imbedded in orattached to other oligonucleotides or polynucleotides to form a largeroligomer which is “partially amidated.” A subject oligonucleotideN3′→P5′ phosphoramidate may include any convenient 3′ and/or 5′ terminalgroups. In some embodiments, the oligonucleotide N3′→P5′ phosphoramidateincludes a 3′-hydroxyl terminal group or a 3′-amino terminal group.

As used herein, the terms “phosphate” and “phosphate group” are meant toencompass a thiophosphate group and an oxophosphate group.

As used herein, the term “phosphoramidite amino group” refers to theamino group, —NR⁴R⁵, attached to the phosphorus atom of aphosphoramidite group, and the term “phosphoramidite nitrogen” refers tothe nitrogen atom of the phosphoramidite amino group.

“Alkyl” refers to monovalent saturated aliphatic hydrocarbyl groupshaving from 1 to 10 carbon atoms and such as 1 to 6 carbon atoms (e.g.,“an alkyl of 1 to 6 carbons atoms”), or 1 to 5 (e.g., “an alkyl of 1 to5 carbons atoms”), or 1 to 4 (e.g., “an alkyl of 1 to 4 carbons atoms”),or 1 to 3 carbon atoms (e.g., “an alkyl of 1 to 3 carbons atoms”). Thisterm includes, by way of example, linear and branched hydrocarbyl groupssuch as methyl (CH₃—), ethyl (CH₃CH₂—), n-propyl (CH₃CH₂CH₂—), isopropyl((CH₃)₂CH—), n-butyl (CH₃CH₂CH₂CH₂—), isobutyl ((CH₃)₂CHCH₂—), sec-butyl((CH₃)(CH₃CH₂)CH—), t-butyl ((CH₃)₃C—), n-pentyl (CH₃CH₂CH₂CH₂CH₂—), andneopentyl ((CH₃)₃CCH₂—).

The term “substituted alkyl” refers to an alkyl group as defined hereinwherein one or more carbon atoms in the alkyl chain have been optionallyreplaced with a heteroatom such as —O—, —N—, —S—, —S(O)_(n)— (where n is0 to 2), —NR— (where R is hydrogen or alkyl) and having from 1 to 5substituents selected from the group consisting of alkoxy, substitutedalkoxy, cycloalkyl, substituted cycloalkyl, cycloalkenyl, substitutedcycloalkenyl, acyl, acylamino, acyloxy, amino, aminoacyl, aminoacyloxy,oxyaminoacyl, azido, cyano, halogen, hydroxyl, oxo, thioketo, carboxyl,carboxylalkyl, thioaryloxy, thioheteroaryloxy, thioheterocyclooxy,thiol, thioalkoxy, substituted thioalkoxy, aryl, aryloxy, heteroaryl,heteroaryloxy, heterocyclyl, heterocyclooxy, hydroxyamino, alkoxyamino,nitro, —SO-alkyl, —SO-aryl, —SO-heteroaryl, —SO₂— alkyl, —SO₂-aryl,—SO₂-heteroaryl, and —NR^(a)R^(b), wherein R^(a) and R^(b) may be thesame or different and are chosen from hydrogen, optionally substitutedalkyl, cycloalkyl, alkenyl, cycloalkenyl, alkynyl, aryl, heteroaryl andheterocyclic. In some instances, a“substituted alkyl” refers to an alkylgroup as defined herein having from 1 to 5 substituents selected fromthe group consisting of alkoxy, cycloalkyl, cycloalkenyl, acyl,acylamino, acyloxy, amino, aminoacyl, aminoacyloxy, oxyaminoacyl, azido,cyano, halogen, hydroxyl, carboxyl, carboxylalkyl, thiol, thioalkoxy,aryl, aryloxy, heteroaryl, heteroaryloxy, heterocyclyl, heterocyclooxy,sulfonamido, and —NR^(a)R^(b), wherein R^(a) and R^(b) may be the sameor different and are chosen from hydrogen, alkyl, cycloalkyl, alkenyl,cycloalkenyl, alkynyl, aryl, heteroaryl and heterocyclic.

“Alkylene” refers to divalent aliphatic hydrocarbyl groups preferablyhaving from 1 to 6 and more preferably 1 to 3 carbon atoms that areeither straight-chained or branched, and which are optionallyinterrupted with one or more groups selected from —O—, —NR¹⁰—,—NR¹⁰C(O)—, —C(O)NR¹⁰— and the like. This term includes, by way ofexample, methylene (—CH₂—), ethylene (—CH₂CH₂—), n-propylene(—CH₂CH₂CH₂—), iso-propylene (—CH₂CH(CH₃)—), (—C(CH₃)₂CH₂CH₂—),(—C(CH₃)₂CH₂C(O)—), (—C(CH₃)₂CH₂C(O)NH—), (—CH(CH₃)CH₂—), and the like.

“Substituted alkylene” refers to an alkylene group having from 1 to 3hydrogens replaced with substituents as described for carbons in thedefinition of “substituted” below.

The term “alkane” refers to alkyl group and alkylene group, as definedherein.

The term “alkylaminoalkyl”, “alkylaminoalkenyl” and “alkylaminoalkynyl”refers to the groups R′ NHR″—where R′ is alkyl group as defined hereinand R″ is alkylene, alkenylene or alkynylene group as defined herein.

The term “alkaryl” or “aralkyl” refers to the groups -alkylene-aryl and-substituted alkylene-aryl where alkylene, substituted alkylene and arylare defined herein.

“Alkoxy” refers to the group —O-alkyl, wherein alkyl is as definedherein. Alkoxy includes, by way of example, methoxy, ethoxy, n-propoxy,isopropoxy, n-butoxy, t-butoxy, sec-butoxy, n-pentoxy, and the like. Theterm “alkoxy” also refers to the groups alkenyl-O—, cycloalkyl-O—,cycloalkenyl-O—, and alkynyl-O—, where alkenyl, cycloalkyl,cycloalkenyl, and alkynyl are as defined herein.

The term “substituted alkoxy” refers to the groups substituted alkyl-O—,substituted alkenyl-O—, substituted cycloalkyl-O—, substitutedcycloalkenyl-O—, and substituted alkynyl-O-where substituted alkyl,substituted alkenyl, substituted cycloalkyl, substituted cycloalkenyland substituted alkynyl are as defined herein.

The term “alkoxyamino” refers to the group —NH-alkoxy, wherein alkoxy isdefined herein.

The term “haloalkoxy” refers to the groups alkyl-O— wherein one or morehydrogen atoms on the alkyl group have been substituted with a halogroup and include, by way of examples, groups such as trifluoromethoxy,and the like.

The term “haloalkyl” refers to a substituted alkyl group as describedabove, wherein one or more hydrogen atoms on the alkyl group have beensubstituted with a halo group. Examples of such groups include, withoutlimitation, fluoroalkyl groups, such as trifluoromethyl, difluoromethyl,trifluoroethyl and the like.

The term “alkylalkoxy” refers to the groups -alkylene-O-alkyl,alkylene-O-substituted alkyl, substituted alkylene-O-alkyl, andsubstituted alkylene-O-substituted alkyl wherein alkyl, substitutedalkyl, alkylene and substituted alkylene are as defined herein.

The term “alkylthioalkoxy” refers to the group -alkylene-S-alkyl,alkylene-S-substituted alkyl, substituted alkylene-S-alkyl andsubstituted alkylene-S-substituted alkyl wherein alkyl, substitutedalkyl, alkylene and substituted alkylene are as defined herein.

“Alkenyl” refers to straight chain or branched hydrocarbyl groups havingfrom 2 to 6 carbon atoms and preferably 2 to 4 carbon atoms and havingat least 1 and preferably from 1 to 2 sites of double bond unsaturation.This term includes, by way of example, bi-vinyl, allyl, andbut-3-en-1-yl. Included within this term are the cis and trans isomersor mixtures of these isomers.

The term “substituted alkenyl” refers to an alkenyl group as definedherein having from 1 to 5 substituents, or from 1 to 3 substituents,selected from alkoxy, substituted alkoxy, cycloalkyl, substitutedcycloalkyl, cycloalkenyl, substituted cycloalkenyl, acyl, acylamino,acyloxy, amino, substituted amino, aminoacyl, aminoacyloxy,oxyaminoacyl, azido, cyano, halogen, hydroxyl, oxo, thioketo, carboxyl,carboxylalkyl, thioaryloxy, thioheteroaryloxy, thioheterocyclooxy,thiol, thioalkoxy, substituted thioalkoxy, aryl, aryloxy, heteroaryl,heteroaryloxy, heterocyclyl, heterocyclooxy, hydroxyamino, alkoxyamino,nitro, —SO-alkyl, —SO— substituted alkyl, —SO-aryl, —SO-heteroaryl,—SO₂-alkyl, —SO₂-substituted alkyl, —SO₂-aryl and —SO₂-heteroaryl.

“Alkynyl” refers to straight or branched monovalent hydrocarbyl groupshaving from 2 to 6 carbon atoms and preferably 2 to 3 carbon atoms andhaving at least 1 and preferably from 1 to 2 sites of triple bondunsaturation. Examples of such alkynyl groups include acetylenyl(—C≡CH), and propargyl (—CH₂C≡CH).

The term “substituted alkynyl” refers to an alkynyl group as definedherein having from 1 to 5 substituents, or from 1 to 3 substituents,selected from alkoxy, substituted alkoxy, cycloalkyl, substitutedcycloalkyl, cycloalkenyl, substituted cycloalkenyl, acyl, acylamino,acyloxy, amino, substituted amino, aminoacyl, aminoacyloxy,oxyaminoacyl, azido, cyano, halogen, hydroxyl, oxo, thioketo, carboxyl,carboxylalkyl, thioaryloxy, thioheteroaryloxy, thioheterocyclooxy,thiol, thioalkoxy, substituted thioalkoxy, aryl, aryloxy, heteroaryl,heteroaryloxy, heterocyclyl, heterocyclooxy, hydroxyamino, alkoxyamino,nitro, —SO-alkyl, —SO— substituted alkyl, —SO-aryl, —SO-heteroaryl,—SO₂-alkyl, —SO₂-substituted alkyl, —SO₂-aryl, and —SO₂-heteroaryl.

“Alkynyloxy” refers to the group —O-alkynyl, wherein alkynyl is asdefined herein. Alkynyloxy includes, by way of example, ethynyloxy,propynyloxy, and the like.

“Acyl” refers to the groups H—C(O)—, alkyl-C(O)—, substitutedalkyl-C(O)—, alkenyl-C(O)—, substituted alkenyl-C(O)—, alkynyl-C(O)—,substituted alkynyl-C(O)—, cycloalkyl-C(O)—, substitutedcycloalkyl-C(O)—, cycloalkenyl-C(O)—, substituted cycloalkenyl-C(O)—,aryl-C(O)—, substituted aryl-C(O)—, heteroaryl-C(O)—, substitutedheteroaryl-C(O)—, heterocyclyl-C(O)—, and substitutedheterocyclyl-C(O)—, wherein alkyl, substituted alkyl, alkenyl,substituted alkenyl, alkynyl, substituted alkynyl, cycloalkyl,substituted cycloalkyl, cycloalkenyl, substituted cycloalkenyl, aryl,substituted aryl, heteroaryl, substituted heteroaryl, heterocyclic, andsubstituted heterocyclic are as defined herein. For example, acylincludes the “acetyl” group CH₃C(O)—

“Acylamino” refers to the groups —NR²⁰C(O)alkyl, —NR²⁰C(O)substitutedalkyl, N R²⁰C(O)cycloalkyl, —NR²⁰C(O)substituted cycloalkyl,—NR²⁰C(O)cycloalkenyl, —NR²⁰C(O)substituted cycloalkenyl,—NR²⁰C(O)alkenyl, —NR²⁰C(O)substituted alkenyl, —NR²⁰C(O)alkynyl,—NR²⁰C(O)substituted alkynyl, —NR²⁰C(O)aryl, —NR²⁰C(O)substituted aryl,—NR²⁰C(O)heteroaryl, —NR²⁰C(O)substituted heteroaryl,—NR²⁰C(O)heterocyclic, and —NR²⁰C(O)substituted heterocyclic, whereinR²⁰ is hydrogen or alkyl and wherein alkyl, substituted alkyl, alkenyl,substituted alkenyl, alkynyl, substituted alkynyl, cycloalkyl,substituted cycloalkyl, cycloalkenyl, substituted cycloalkenyl, aryl,substituted aryl, heteroaryl, substituted heteroaryl, heterocyclic, andsubstituted heterocyclic are as defined herein.

“Aminocarbonyl” or the term “aminoacyl” refers to the group—C(O)NR²¹R²², wherein R²¹ and R²² independently are selected from thegroup consisting of hydrogen, alkyl, substituted alkyl, alkenyl,substituted alkenyl, alkynyl, substituted alkynyl, aryl, substitutedaryl, cycloalkyl, substituted cycloalkyl, cycloalkenyl, substitutedcycloalkenyl, heteroaryl, substituted heteroaryl, heterocyclic, andsubstituted heterocyclic and where R²¹ and R²² are optionally joinedtogether with the nitrogen bound thereto to form a heterocyclic orsubstituted heterocyclic group, and wherein alkyl, substituted alkyl,alkenyl, substituted alkenyl, alkynyl, substituted alkynyl, cycloalkyl,substituted cycloalkyl, cycloalkenyl, substituted cycloalkenyl, aryl,substituted aryl, heteroaryl, substituted heteroaryl, heterocyclic, andsubstituted heterocyclic are as defined herein.

“Aminocarbonylamino” refers to the group —NR²¹C(O)NR²²R²³ where R²¹,R²², and R²³ are independently selected from hydrogen, alkyl, aryl orcycloalkyl, or where two R groups are joined to form a heterocyclylgroup.

The term “alkoxycarbonylamino” refers to the group —NRC(O)OR where eachR is independently hydrogen, alkyl, substituted alkyl, aryl, heteroaryl,or heterocyclyl wherein alkyl, substituted alkyl, aryl, heteroaryl, andheterocyclyl are as defined herein.

The term “acyloxy” refers to the groups alkyl-C(O)O—, substitutedalkyl-C(O)O—, cycloalkyl-C(O)O—, substituted cycloalkyl-C(O)O—,aryl-C(O)O—, heteroaryl-C(O)O—, and heterocyclyl-C(O)O— wherein alkyl,substituted alkyl, cycloalkyl, substituted cycloalkyl, aryl, heteroaryl,and heterocyclyl are as defined herein.

“Aminosulfonyl” refers to the group —SO₂NR²¹R²², wherein R²¹ and R²²independently are selected from the group consisting of hydrogen, alkyl,substituted alkyl, alkenyl, substituted alkenyl, alkynyl, substitutedalkynyl, aryl, substituted aryl, cycloalkyl, substituted cycloalkyl,cycloalkenyl, substituted cycloalkenyl, heteroaryl, substitutedheteroaryl, heterocyclic, substituted heterocyclic and where R²¹ and R²²are optionally joined together with the nitrogen bound thereto to form aheterocyclic or substituted heterocyclic group and alkyl, substitutedalkyl, alkenyl, substituted alkenyl, alkynyl, substituted alkynyl,cycloalkyl, substituted cycloalkyl, cycloalkenyl, substitutedcycloalkenyl, aryl, substituted aryl, heteroaryl, substitutedheteroaryl, heterocyclic and substituted heterocyclic are as definedherein.

“Sulfonylamino” refers to the group —NR²¹SO₂R²², wherein R²¹ and R²²independently are selected from the group consisting of hydrogen, alkyl,substituted alkyl, alkenyl, substituted alkenyl, alkynyl, substitutedalkynyl, aryl, substituted aryl, cycloalkyl, substituted cycloalkyl,cycloalkenyl, substituted cycloalkenyl, heteroaryl, substitutedheteroaryl, heterocyclic, and substituted heterocyclic and where R²¹ andR²² are optionally joined together with the atoms bound thereto to forma heterocyclic or substituted heterocyclic group, and wherein alkyl,substituted alkyl, alkenyl, substituted alkenyl, alkynyl, substitutedalkynyl, cycloalkyl, substituted cycloalkyl, cycloalkenyl, substitutedcycloalkenyl, aryl, substituted aryl, heteroaryl, substitutedheteroaryl, heterocyclic, and substituted heterocyclic are as definedherein.

“Aryl” or “Ar” refers to a monovalent aromatic carbocyclic group of from6 to 18 carbon atoms having a single ring (such as is present in aphenyl group) or a ring system having multiple condensed rings (examplesof such aromatic ring systems include naphthyl, anthryl and indanyl)which condensed rings may or may not be aromatic, provided that thepoint of attachment is through an atom of an aromatic ring. This termincludes, by way of example, phenyl and naphthyl. Unless otherwiseconstrained by the definition for the aryl substituent, such aryl groupscan optionally be substituted with from 1 to 5 substituents, or from 1to 3 substituents, selected from acyloxy, hydroxy, thiol, acyl, alkyl,alkoxy, alkenyl, alkynyl, cycloalkyl, cycloalkenyl, substituted alkyl,substituted alkoxy, substituted alkenyl, substituted alkynyl,substituted cycloalkyl, substituted cycloalkenyl, amino, substitutedamino, aminoacyl, acylamino, alkaryl, aryl, aryloxy, azido, carboxyl,carboxylalkyl, cyano, halogen, nitro, heteroaryl, heteroaryloxy,heterocyclyl, heterocyclooxy, aminoacyloxy, oxyacylamino, thioalkoxy,substituted thioalkoxy, thioaryloxy, thioheteroaryloxy, —SO-alkyl,—SO-substituted alkyl, —SO-aryl, —SO-heteroaryl, —SO₂-alkyl,—SO₂-substituted alkyl, —SO₂-aryl, —SO₂-heteroaryl and trihalomethyl. Insuch cases, an aryl group that is substituted with from 1 to 5substituents (e.g., as described herein) is referred to as a“substituted aryl”.

“Aryloxy” refers to the group —O-aryl, wherein aryl is as definedherein, including, by way of example, phenoxy, naphthoxy, and the like,including optionally substituted aryl groups as also defined herein.

“Amino” refers to the group —NH₂.

The term “substituted amino” refers to the group —NRR where each R isindependently selected from the group consisting of hydrogen, alkyl,substituted alkyl, cycloalkyl, substituted cycloalkyl, alkenyl,substituted alkenyl, cycloalkenyl, substituted cycloalkenyl, alkynyl,substituted alkynyl, aryl, heteroaryl, and heterocyclyl provided that atleast one R is not hydrogen.

The term “azido” refers to the group —N₃.

“Carboxyl,” “carboxy” or “carboxylate” refers to —CO₂H or salts thereof.

“Carboxyl ester” or “carboxy ester” or the terms “carboxyalkyl” or“carboxylalkyl” refers to the groups —C(O)O-alkyl, —C(O)O-substitutedalkyl, —C(O)O-alkenyl, —C(O)O-substituted alkenyl, —C(O)O-alkynyl,—C(O)O-substituted alkynyl, —C(O)O-aryl, —C(O)O-substituted aryl,—C(O)O-cycloalkyl, —C(O)O-substituted cycloalkyl, —C(O)O-cycloalkenyl,—C(O)O-substituted cycloalkenyl, —C(O)O-heteroaryl, —C(O)O-substitutedheteroaryl, —C(O)O-heterocyclic, and —C(O)O-substituted heterocyclic,wherein alkyl, substituted alkyl, alkenyl, substituted alkenyl, alkynyl,substituted alkynyl, cycloalkyl, substituted cycloalkyl, cycloalkenyl,substituted cycloalkenyl, aryl, substituted aryl, heteroaryl,substituted heteroaryl, heterocyclic, and substituted heterocyclic areas defined herein.

“(Carboxyl ester)oxy” or “carbonate” refers to the groups —O—C(O)O—alkyl, —O—C(O)O-substituted alkyl, —O—C(O)O-alkenyl,—O—C(O)O-substituted alkenyl, —O—C(O)O-alkynyl, —O—C(O)O-substitutedalkynyl, —O—C(O)O-aryl, —O—C(O)O-substituted aryl, —O—C(O)O-cycloalkyl,—O—C(O)O-substituted cycloalkyl, —O—C(O)O-cycloalkenyl, —O—C(O)O—substituted cycloalkenyl, —O—C(O)O-heteroaryl, —O—C(O)O-substitutedheteroaryl, —O—C(O)O-heterocyclic, and —O—C(O)O-substitutedheterocyclic, wherein alkyl, substituted alkyl, alkenyl, substitutedalkenyl, alkynyl, substituted alkynyl, cycloalkyl, substitutedcycloalkyl, cycloalkenyl, substituted cycloalkenyl, aryl, substitutedaryl, heteroaryl, substituted heteroaryl, heterocyclic, and substitutedheterocyclic are as defined herein.

“Cyano” or “nitrile” refers to the group —CN.

“Cycloalkyl” refers to cyclic alkyl groups of from 3 to 10 carbon atomshaving single or multiple cyclic rings including fused, bridged, andspiro ring systems. Examples of suitable cycloalkyl groups include, forinstance, adamantyl, cyclopropyl, cyclobutyl, cyclopentyl, cyclooctyland the like. Such cycloalkyl groups include, by way of example, singlering structures such as cyclopropyl, cyclobutyl, cyclopentyl,cyclooctyl, and the like, or multiple ring structures such asadamantanyl, and the like.

The term “substituted cycloalkyl” refers to cycloalkyl groups havingfrom 1 to 5 substituents, or from 1 to 3 substituents, selected fromalkyl, substituted alkyl, alkoxy, substituted alkoxy, cycloalkyl,substituted cycloalkyl, cycloalkenyl, substituted cycloalkenyl, acyl,acylamino, acyloxy, amino, substituted amino, aminoacyl, aminoacyloxy,oxyaminoacyl, azido, cyano, halogen, hydroxyl, oxo, thioketo, carboxyl,carboxylalkyl, thioaryloxy, thioheteroaryloxy, thioheterocyclooxy,thiol, thioalkoxy, substituted thioalkoxy, aryl, aryloxy, heteroaryl,heteroaryloxy, heterocyclyl, heterocyclooxy, hydroxyamino, alkoxyamino,nitro, —SO-alkyl, —SO-substituted alkyl, —SO-aryl, —SO-heteroaryl,—SO₂-alkyl, —SO₂-substituted alkyl, —SO₂-aryl and —SO₂-heteroaryl.

“Cycloalkenyl” refers to non-aromatic cyclic alkyl groups of from 3 to10 carbon atoms having single or multiple rings and having at least onedouble bond and preferably from 1 to 2 double bonds.

The term “substituted cycloalkenyl” refers to cycloalkenyl groups havingfrom 1 to 5 substituents, or from 1 to 3 substituents, selected fromalkoxy, substituted alkoxy, cycloalkyl, substituted cycloalkyl,cycloalkenyl, substituted cycloalkenyl, acyl, acylamino, acyloxy, amino,substituted amino, aminoacyl, aminoacyloxy, oxyaminoacyl, azido, cyano,halogen, hydroxyl, keto, thioketo, carboxyl, carboxylalkyl, thioaryloxy,thioheteroaryloxy, thioheterocyclooxy, thiol, thioalkoxy, substitutedthioalkoxy, aryl, aryloxy, heteroaryl, heteroaryloxy, heterocyclyl,heterocyclooxy, hydroxyamino, alkoxyamino, nitro, —SO-alkyl,—SO-substituted alkyl, —SO-aryl, —SO-heteroaryl, —SO₂-alkyl,—SO₂-substituted alkyl, —SO₂-aryl and —SO₂-heteroaryl.

“Cycloalkynyl” refers to non-aromatic cycloalkyl groups of from 5 to 10carbon atoms having single or multiple rings and having at least onetriple bond.

“Cycloalkoxy” refers to —O-cycloalkyl.

“Cycloalkenyloxy” refers to —O-cycloalkenyl.

“Halo” or “halogen” refers to fluoro, chloro, bromo, and iodo.

“Hydroxy” or “hydroxyl” refers to the group —OH.

“Heteroaryl” refers to an aromatic group of from 1 to 15 carbon atoms,such as from 1 to 10 carbon atoms and 1 to 10 heteroatoms selected fromthe group consisting of oxygen, nitrogen, and sulfur within the ring.Such heteroaryl groups can have a single ring (such as, pyridinyl,imidazolyl or furyl) or multiple condensed rings in a ring system (forexample as in groups such as, indolizinyl, quinolinyl, benzofuran,benzimidazolyl or benzothienyl), wherein at least one ring within thering system is aromatic and at least one ring within the ring system isaromatic, provided that the point of attachment is through an atom of anaromatic ring. In certain embodiments, the nitrogen and/or sulfur ringatom(s) of the heteroaryl group are optionally oxidized to provide forthe N-oxide (N→O), sulfinyl, or sulfonyl moieties. This term includes,by way of example, pyridinyl, pyrrolyl, indolyl, thiophenyl, andfuranyl. Unless otherwise constrained by the definition for theheteroaryl substituent, such heteroaryl groups can be optionallysubstituted with 1 to 5 substituents, or from 1 to 3 substituents,selected from acyloxy, hydroxy, thiol, acyl, alkyl, alkoxy, alkenyl,alkynyl, cycloalkyl, cycloalkenyl, substituted alkyl, substitutedalkoxy, substituted alkenyl, substituted alkynyl, substitutedcycloalkyl, substituted cycloalkenyl, amino, substituted amino,aminoacyl, acylamino, alkaryl, aryl, aryloxy, azido, carboxyl,carboxylalkyl, cyano, halogen, nitro, heteroaryl, heteroaryloxy,heterocyclyl, heterocyclooxy, aminoacyloxy, oxyacylamino, thioalkoxy,substituted thioalkoxy, thioaryloxy, thioheteroaryloxy, —SO-alkyl,—SO-substituted alkyl, —SO-aryl, —SO-heteroaryl, —SO₂-alkyl,—SO₂-substituted alkyl, —SO₂-aryl and —SO₂-heteroaryl, andtrihalomethyl. In such cases, a heteroaryl group that is substitutedwith from 1 to 5 substituents (e.g., as described herein) is referred toas a “substituted heteroaryl”.

The term “heteroaralkyl” refers to the groups -alkylene-heteroaryl wherealkylene and heteroaryl are defined herein. This term includes, by wayof example, pyridylmethyl, pyridylethyl, indolylmethyl, and the like.

“Heteroaryloxy” refers to —O-heteroaryl.

“Heterocycle,” “heterocyclic,” “heterocycloalkyl,” and “heterocyclyl”refer to a saturated or unsaturated group having a single ring ormultiple condensed rings, including fused bridged and spiro ringsystems, and having from 3 to 20 ring atoms, including 1 to 10 heteroatoms. These ring atoms are selected from the group consisting ofnitrogen, sulfur, or oxygen, wherein, in fused ring systems, one or moreof the rings can be cycloalkyl, aryl, or heteroaryl, provided that thepoint of attachment is through the non-aromatic ring. In certainembodiments, the nitrogen and/or sulfur atom(s) of the heterocyclicgroup are optionally oxidized to provide for the N-oxide, —S(O)—, or—SO₂— moieties.

Examples of heterocycles and heteroaryls include, but are not limitedto, azetidine, pyrrole, imidazole, pyrazole, pyridine, pyrazine,pyrimidine, pyridazine, indolizine, isoindole, indole, dihydroindole,indazole, purine, quinolizine, isoquinoline, quinoline, phthalazine,naphthylpyridine, quinoxaline, quinazoline, cinnoline, pteridine,carbazole, carboline, phenanthridine, acridine, phenanthroline,isothiazole, phenazine, isoxazole, phenoxazine, phenothiazine,imidazolidine, imidazoline, piperidine, piperazine, indoline,phthalimide, 1,2,3,4-tetrahydroisoquinoline,4,5,6,7-tetrahydrobenzo[b]thiophene, thiazole, thiazolidine, thiophene,benzo[b]thiophene, morpholinyl, thiomorpholinyl (also referred to asthiamorpholinyl), 1,1-dioxothiomorpholinyl, piperidinyl, pyrrolidine,tetrahydrofuranyl, and the like.

Unless otherwise constrained by the definition for the heterocyclicsubstituent, such heterocyclic groups can be optionally substituted with1 to 5, or from 1 to 3 substituents, selected from alkoxy, substitutedalkoxy, cycloalkyl, substituted cycloalkyl, cycloalkenyl, substitutedcycloalkenyl, acyl, acylamino, acyloxy, amino, substituted amino,aminoacyl, aminoacyloxy, oxyaminoacyl, azido, cyano, halogen, hydroxyl,oxo, thioketo, carboxyl, carboxylalkyl, thioaryloxy, thioheteroaryloxy,thioheterocyclooxy, thiol, thioalkoxy, substituted thioalkoxy, aryl,aryloxy, heteroaryl, heteroaryloxy, heterocyclyl, heterocyclooxy,hydroxyamino, alkoxyamino, nitro, —SO-alkyl, —SO-substituted alkyl,—SO-aryl, —SO-heteroaryl, —SO₂-alkyl, —SO₂-substituted alkyl, —SO₂-aryl,—SO₂-heteroaryl, and fused heterocycle.

“Heterocyclyloxy” refers to the group —O-heterocyclyl.

The term “heterocyclylthio” refers to the group heterocyclic-S—.

The term “heterocyclene” refers to the diradical group formed from aheterocycle, as defined herein.

The term “hydroxyamino” refers to the group —NHOH.

“Nitro” refers to the group —NO₂.

“Oxo” refers to the atom (═O).

“Sulfonyl” refers to the group SO₂-alkyl, SO₂-substituted alkyl,SO₂-alkenyl, SO₂-substituted alkenyl, SO₂-cycloalkyl, SO₂-substitutedcycloalkyl, SO₂-cycloalkenyl, SO₂-substituted cylcoalkenyl, SO₂-aryl,SO₂-substituted aryl, SO₂-heteroaryl, SO₂-substituted heteroaryl,SO₂-heterocyclic, and SO₂-substituted heterocyclic, wherein alkyl,substituted alkyl, alkenyl, substituted alkenyl, alkynyl, substitutedalkynyl, cycloalkyl, substituted cycloalkyl, cycloalkenyl, substitutedcycloalkenyl, aryl, substituted aryl, heteroaryl, substitutedheteroaryl, heterocyclic, and substituted heterocyclic are as definedherein. Sulfonyl includes, by way of example, methyl-SO₂—, phenyl-SO₂—,and 4-methylphenyl-SO₂—.

“Sulfonyloxy” refers to the group —OSO₂-alkyl, OSO₂-substituted alkyl,OSO₂-alkenyl, OSO₂-substituted alkenyl, OSO₂-cycloalkyl,OSO₂-substituted cycloalkyl, OSO₂-cycloalkenyl, OSO₂-substitutedcylcoalkenyl, OSO₂-aryl, OSO₂-substituted aryl, OSO₂-heteroaryl,OSO₂-substituted heteroaryl, OSO₂-heterocyclic, and OSO₂ substitutedheterocyclic, wherein alkyl, substituted alkyl, alkenyl, substitutedalkenyl, alkynyl, substituted alkynyl, cycloalkyl, substitutedcycloalkyl, cycloalkenyl, substituted cycloalkenyl, aryl, substitutedaryl, heteroaryl, substituted heteroaryl, heterocyclic, and substitutedheterocyclic are as defined herein.

The term “aminocarbonyloxy” refers to the group —OC(O)NRR where each Ris independently hydrogen, alkyl, substituted alkyl, aryl, heteroaryl,or heterocyclic wherein alkyl, substituted alkyl, aryl, heteroaryl andheterocyclic are as defined herein.

“Thiol” refers to the group —SH.

“Thioxo” or the term “thioketo” refers to the atom (═S).

“Alkylthio” or the term “thioalkoxy” refers to the group —S-alkyl,wherein alkyl is as defined herein. In certain embodiments, sulfur maybe oxidized to —S(O)—. The sulfoxide may exist as one or morestereoisomers.

The term “substituted thioalkoxy” refers to the group —S-substitutedalkyl.

The term “thioaryloxy” refers to the group aryl-S— wherein the arylgroup is as defined herein including optionally substituted aryl groupsalso defined herein.

The term “thioheteroaryloxy” refers to the group heteroaryl-S— whereinthe heteroaryl group is as defined herein including optionallysubstituted aryl groups as also defined herein.

The term “thioheterocyclooxy” refers to the group heterocyclyl-S—wherein the heterocyclyl group is as defined herein including optionallysubstituted heterocyclyl groups as also defined herein.

In addition to the disclosure herein, the term “substituted,” when usedto modify a specified group or radical, can also mean that one or morehydrogen atoms of the specified group or radical are each, independentlyof one another, replaced with the same or different substituent groupsas defined below.

In addition to the groups disclosed with respect to the individual termsherein, substituent groups for substituting for one or more hydrogens(any two hydrogens on a single carbon can be replaced with ═O, ═NR⁷⁰,═N—OR⁷⁰, ═N₂ or ═S) on saturated carbon atoms in the specified group orradical are, unless otherwise specified, —R⁶⁰, halo, ═O, —OR⁷⁰, —SR⁷⁰,—NR⁸⁰R⁸⁰ trihalomethyl, —CN, —OCN, —SCN, —NO, —NO₂, ═N₂, —N₃, —SO₂R⁷⁰,—SO₂O⁻M⁺, —SO₂OR⁷⁰, —OSO₂R⁷⁰, —OSO₂O⁻M⁺, —OSO₂OR⁷⁰, —P(O)(O⁻)₂(M⁺)₂,—P(O)(OR⁷⁰)O⁻M⁺, —P(O)(OR⁷⁰)₂, —C(O)R⁷⁰, —C(S)R⁷⁰, —C(NR⁷⁰)R⁷⁰,—C(O)O⁻M⁺, —C(O)OR⁷⁰, —C(S)OR⁷⁰, —C(O)NR⁸⁰R⁸⁰, —C(NR⁷⁰)NR⁸⁰R⁸⁰,—OC(O)R⁷⁰, —OC(S)R⁷⁰, —OC(O)O⁻M⁺, —OC(O)OR⁷⁰, —OC(S)OR⁷⁰, —NR⁷⁰C(O)R⁷⁰,—NR⁷⁰C(S)R⁷⁰, —NR⁷⁰CO₂ ⁻M⁺, —NR⁷⁰CO₂R⁷⁰, —NR⁷⁰C(S)OR⁷⁰,—NR⁷⁰C(O)NR⁸⁰R⁸⁰, —NR⁷⁰C(NR⁷⁰)R⁷⁰ and —NR⁷⁰C(NR⁷⁰)NR⁸⁰R⁸⁰, where R⁶⁰ isselected from the group consisting of optionally substituted alkyl,cycloalkyl, heteroalkyl, heterocycloalkylalkyl, cycloalkylalkyl, aryl,arylalkyl, heteroaryl and heteroarylalkyl, each R⁷⁰ is independentlyhydrogen or R⁶⁰; each R⁸⁰ is independently R⁷⁰ or alternatively, twoR⁸⁰'s, taken together with the nitrogen atom to which they are bonded,form a 5-, 6- or 7-membered heterocycloalkyl which may optionallyinclude from 1 to 4 of the same or different additional heteroatomsselected from the group consisting of 0, N and S, of which N may have —Hor C₁-C₃ alkyl substitution; and each M⁺ is a counter ion with a netsingle positive charge. Each M⁺ may independently be, for example, analkali ion, such as K⁺, Na⁺, Li⁺; an ammonium ion, such as +N(R⁶⁰)₄; oran alkaline earth ion, such as [Ca²⁺]_(0.5), [Mg²⁺]_(0.5), or[Ba²⁺]_(0.5) (“subscript 0.5 means that one of the counter ions for suchdivalent alkali earth ions can be an ionized form of a compound of theinvention and the other a counter ion such as chloride, or two ionizedcompounds disclosed herein can serve as counter ions for such divalentalkali earth ions, or a doubly ionized compound of the invention canserve as the counter ion for such divalent alkali earth ions). Asspecific examples, —NR⁸⁰R⁸⁰ is meant to include —NH₂, —NH-alkyl,N-pyrrolidinyl, N-piperazinyl, 4N-methyl-piperazin-1-yl andN-morpholinyl.

In addition to the disclosure herein, substituent groups for hydrogenson unsaturated carbon atoms in “substituted” alkene, alkyne, aryl andheteroaryl groups are, unless otherwise specified, —R⁶⁰, halo, —O⁻M⁺,—OR⁷⁰, —SR⁷⁰, —S⁻M⁺, —NR⁸⁰R⁸⁰,

trihalomethyl, —CF₃, —CN, —OCN, —SCN, —NO, —NO₂, —N₃, —SO₂R⁷⁰, —SO₃ ⁻M⁺, —SO₃R⁷⁰, —OSO₂R⁷⁰, —OSO₃ ⁻M⁺, —OSO₃R⁷⁰, —PO₃ ⁻²(M⁺)₂, —P(O)(OR⁷⁰)O⁻M⁺, —P(O)(OR⁷⁰)₂, —C(O)R⁷⁰, —C(S)R⁷⁰, —C(NR⁷⁰)R⁷⁰, —CO₂ ⁻M⁺, —CO₂R⁷⁰, —C(S)OR⁷⁰, —C(O)NR⁸⁰R⁸⁰, —C(NR⁷⁰)NR⁸⁰R⁸⁰, —OC(O)R⁷⁰,—OC(S)R⁷⁰, —OCO₂ ⁻M⁺, —OCO₂R⁷⁰, —OC(S)OR⁷⁰, —NR⁷⁰C(O)R⁷⁰, —NR⁷⁰C(S)R⁷⁰, —NR⁷⁰CO₂ ⁻M⁺, —NR⁷⁰CO₂R⁷⁰, —NR⁷⁰C(S)OR⁷⁰, —NR⁷⁰C(O)NR⁸⁰R⁸⁰, —NR⁷C(NR⁷⁰)R⁷⁰and —NR⁷⁰C(NR⁷⁰)NR⁸⁰R⁸⁰, where R⁶⁰, R⁷⁰, R⁸⁰ and M⁺ are as previouslydefined, provided that in case of substituted alkene or alkyne, thesubstituents are not —O⁻M⁺, —OR⁷⁰, —SR⁷⁰, or —S⁻M⁺.

In addition to the groups disclosed with respect to the individual termsherein, substituent groups for hydrogens on nitrogen atoms in“substituted” heteroalkyl and cycloheteroalkyl groups are, unlessotherwise

specified, —R⁶⁰, —O⁻M⁺, —OR⁷⁰, —SR⁷⁰, —S⁻M⁺, —NR⁸⁰R⁸⁰trihalomethyl, —CF₃, —CN, —NO, —NO₂, —S(O)₂R⁷⁰, —S(O)₂O⁻M⁺, —S(O)₂OR⁷⁰,—OS(O)₂R⁷⁰, —OS(O)₂O⁻M⁺, —OS(O)₂OR⁷⁰, —P(O)(O⁻)₂(M⁺)₂, —P(O)(OR⁷⁰)O⁻M⁺,—P(O)(OR⁷⁰)(OR⁷⁰), —C(O)R⁷⁰, —C(S)R⁷⁰, —C(NR⁷⁰)R⁷⁰, —C(O)OR⁷⁰,—C(S)OR⁷⁰, —C(O)NR⁸⁰R⁸⁰, —C(NR⁷⁰)NR⁸⁰R⁸⁰, —OC(O)R⁷⁰, —OC(S)R⁷⁰,—OC(O)OR⁷⁰, —OC(S)OR⁷⁰, —NR⁷⁰C(O)R⁷⁰, —NR⁷⁰C(S)R 7, —NR⁷⁰C(O)OR⁷⁰,—NR⁷⁰C(S)OR⁷⁰, —NR⁷⁰C(O)NR⁸⁰R⁸⁰, —NR⁷⁰C(NR⁷⁰)R⁷⁰ and—NR⁷⁰C(NR⁷⁰)NR⁸⁰R⁸⁰, where R⁶⁰, R⁷⁰, R⁸⁰ and M⁺ are as previouslydefined.

In addition to the disclosure herein, in a certain embodiment, a groupthat is substituted has 1, 2, 3, or 4 substituents, 1, 2, or 3substituents, 1 or 2 substituents, or 1 substituent.

It is understood that in all substituted groups defined above, polymersarrived at by defining substituents with further substituents tothemselves (e.g., substituted aryl having a substituted aryl group as asubstituent which is itself substituted with a substituted aryl group,which is further substituted by a substituted aryl group, etc.) are notintended for inclusion herein. In such cases, the maximum number of suchsubstitutions is three. For example, serial substitutions of substitutedaryl groups specifically contemplated herein are limited to substitutedaryl-(substituted aryl)-substituted aryl.

Unless indicated otherwise, the nomenclature of substituents that arenot explicitly defined herein are arrived at by naming the terminalportion of the functionality followed by the adjacent functionalitytoward the point of attachment. For example, the substituent“arylalkyloxycarbonyl” refers to the group (aryl)-(alkyl)-O—C(O)—.

As to any of the groups disclosed herein which contain one or moresubstituents, it is understood, of course, that such groups do notcontain any substitution or substitution patterns which are stericallyimpractical and/or synthetically non-feasible. In addition, the subjectcompounds include all stereochemical isomers arising from thesubstitution of these compounds.

The term “pharmaceutically acceptable salt” means a salt which isacceptable for administration to a patient, such as a mammal (salts withcounterions having acceptable mammalian safety for a given dosageregime). Such salts can be derived from pharmaceutically acceptableinorganic or organic bases and from pharmaceutically acceptableinorganic or organic acids. “Pharmaceutically acceptable salt” refers topharmaceutically acceptable salts of a compound, which salts are derivedfrom a variety of organic and inorganic counter ions well known in theart and include, by way of example only, sodium, and the like; and whenthe molecule contains a basic functionality, salts of organic orinorganic acids, such as hydrochloride, and the like. Pharmaceuticallyacceptable salts of interest include, but are not limited to, aluminium,ammonium, arginine, barium, benzathine, calcium, cholinate,ethylenediamine, lysine, lithium, magnesium, meglumine, procaine,potassium, sodium, tromethamine, N-methylglucamine,N,N′-dibenzylethylene-diamine, chloroprocaine, diethanolamine,ethanolamine, piperazine, zinc, diisopropylamine, diisopropylethylamine,triethylamine and triethanolamine salts.

The term “salt thereof” means a compound formed when a proton of an acidis replaced by a cation, such as a metal cation or an organic cation andthe like. Where applicable, the salt is a pharmaceutically acceptablesalt, although this is not required for salts of intermediate compoundsthat are not intended for administration to a patient. By way ofexample, salts of the present compounds include those wherein thecompound is protonated by an inorganic or organic acid to form a cation,with the conjugate base of the inorganic or organic acid as the anioniccomponent of the salt. Salts of interest include, but are not limitedto, aluminium, ammonium, arginine, barium, benzathine, calcium, cesium,cholinate, ethylenediamine, lithium, magnesium, meglumine, procaine,N-methylglucamine, piperazine, potassium, sodium, tromethamine, zinc,N,N′-dibenzylethylene-diamine, chloroprocaine, diethanolamine,ethanolamine, piperazine, diisopropylamine, diisopropylethylamine,triethylamine and triethanolamine salts. It is understood that for anyof the oligonucleotide structures depicted herein that include abackbone of intemucleoside linkages, such oligonucleotides may alsoinclude any convenient salt forms. In some embodiments, acidic forms ofthe intemucleoside linkages are depicted for simplicity. In someinstances, the salt of the subject compound is a monovalent cation salt.In certain instances, the salt of the subject compound is a divalentcation salt. In some instances, the salt of the subject compound is atrivalent cation salt. “Solvate” refers to a complex formed bycombination of solvent molecules with molecules or ions of the solute.The solvent can be an organic compound, an inorganic compound, or amixture of both. Some examples of solvents include, but are not limitedto, methanol, N,N-dimethylformamide, tetrahydrofuran, dimethylsulfoxide,and water. When the solvent is water, the solvate formed is a hydrate.

“Stereoisomer” and “stereoisomers” refer to compounds that have sameatomic connectivity but different atomic arrangement in space.Stereoisomers include cis-trans isomers, E and Z isomers, enantiomers,and diastereomers.

“Tautomer” refers to alternate forms of a molecule that differ only inelectronic bonding of atoms and/or in the position of a proton, such asenol-keto and imine-enamine tautomers, —NH—P(═S)(OH)—O— and—NH—P(═O)(SH)—O—, or the tautomeric forms of heteroaryl groupscontaining a —N═C(H)—NH— ring atom arrangement, such as pyrazoles,imidazoles, benzimidazoles, triazoles, and tetrazoles. A person ofordinary skill in the art would recognize that other tautomericarrangements of the groups described herein are possible. For example,it is understood that an oligonucleotide described by the followingstructure:

also encompasses the following structure showing one possible alternatetautomeric arrangement of linkage groups:

where “nps” represents a thiophosphoramidate linkage (—NH—P(═O)(SH)—O orNH P(═S)(OH)—O—) connecting the 3′-carbon of one nucleoside to the5′-carbon of the adjacent nucleoside. It is understood that alltautomeric forms of a subject compound are encompassed by a structurewhere one possible tautomeric arrangement of the groups of the compoundis described, even if not specifically indicated. Any convenienttautomeric arrangement of the groups of the subject compounds may beutilized in describing the compounds.

It will be appreciated that the term “or a salt or solvate orstereoisomer thereof” is intended to include all permutations of salts,solvates and stereoisomers, such as a solvate of a pharmaceuticallyacceptable salt of a stereoisomer of subject compound. It is understoodthat the term “or a salt thereof” is intended to include allpermutations of salts. It is understood that the term “or apharmaceutically acceptable salt thereof” is intended to include allpermutations of salts. It is understood that the term “or a solvatethereof” is intended to include all permutations of solvates. It isunderstood that the term “or a stereoisomer thereof” is intended toinclude all permutations of stereoisomers. It is understood that theterm “or a tautomer thereof” is intended to include all permutations oftautomers. Thus for example it follows that it is intended to include asolvate of a pharmaceutically acceptable salt of a tautomer of astereoisomer of subject compound.

“Pharmaceutically effective amount” and “therapeutically effectiveamount” refer to an amount of a compound sufficient to treat a specifieddisorder or disease or one or more of its symptoms and/or to prevent theoccurrence of the disease or disorder. In reference to tumorigenicproliferative disorders, a pharmaceutically or therapeutically effectiveamount comprises an amount sufficient to, among other things, cause thetumor to shrink or decrease the growth rate of the tumor.

“Patient” refers to human and non-human subjects, especially mammaliansubjects.

The term “treating” or “treatment” as used herein means the treating ortreatment of a disease or medical condition in a patient, such as amammal (particularly a human) that includes: (a) preventing the diseaseor medical condition from occurring, such as, prophylactic treatment ofa subject; (b) ameliorating the disease or medical condition, such as,eliminating or causing regression of the disease or medical condition ina patient; (c) suppressing the disease or medical condition, for exampleby, slowing or arresting the development of the disease or medicalcondition in a patient; or (d) alleviating a symptom of the disease ormedical condition in a patient.

As used herein the term “isolated” is meant to describe a compound ofinterest that is in an environment different from that in which thecompound naturally occurs. “Isolated” is meant to include compounds thatare within samples that are substantially enriched for the compound ofinterest and/or in which the compound of interest is partially orsubstantially purified.

As used herein, the term “substantially purified” refers to a compoundthat is removed from its natural environment and is at least 60% free,at least 75% free, at least 80% free, at least 85% free, at least 90%free, at least 95% free, at least 98% free, or more than 98% free, fromother components with which it is naturally associated.

The term “physiological conditions” is meant to encompass thoseconditions compatible with living cells, e.g., predominantly aqueousconditions of a temperature, pH, salinity, etc. that are compatible withliving cells.

Before the present invention is further described, it is to beunderstood that this invention is not limited to particular embodimentsdescribed, as such may, of course, vary. It is also to be understoodthat the terminology used herein is for the purpose of describingparticular embodiments only, and is not intended to be limiting, sincethe scope of the present invention will be limited only by the appendedclaims.

Where a range of values is provided, it is understood that eachintervening value, to the tenth of the unit of the lower limit unlessthe context clearly dictates otherwise, between the upper and lowerlimit of that range and any other stated or intervening value in thatstated range, is encompassed within the invention. The upper and lowerlimits of these smaller ranges may independently be included in thesmaller ranges, and are also encompassed within the invention, subjectto any specifically excluded limit in the stated range. Where the statedrange includes one or both of the limits, ranges excluding either orboth of those included limits are also included in the invention.

It is appreciated that certain features of the invention, which are, forclarity, described in the context of separate embodiments, may also beprovided in combination in a single embodiment. Conversely, variousfeatures of the invention, which are, for brevity, described in thecontext of a single embodiment, may also be provided separately or inany suitable sub-combination. All combinations of the embodimentspertaining to the invention are specifically embraced by the presentinvention and are disclosed herein just as if each and every combinationwas individually and explicitly disclosed, to the extent that suchcombinations embrace subject matter that are, for example, compoundsthat are stable compounds (i.e., compounds that can be made, isolated,characterized, and tested for biological activity). In addition, allsub-combinations of the various embodiments and elements thereof (e.g.,elements of the chemical groups listed in the embodiments describingsuch variables) are also specifically embraced by the present inventionand are disclosed herein just as if each and every such sub-combinationwas individually and explicitly disclosed herein.

Unless defined otherwise, all technical and scientific terms used hereinhave the same meaning as commonly understood by one of ordinary skill inthe art to which this invention belongs. Although any methods andmaterials similar or equivalent to those described herein can also beused in the practice or testing of the present invention, methods andmaterials of interest are now described. All publications mentionedherein are incorporated herein by reference to disclose and describe themethods and/or materials in connection with which the publications arecited.

It must be noted that as used herein and in the appended claims, thesingular forms “a,” “an,” and “the” include plural referents unless thecontext clearly dictates otherwise. It is further noted that the claimsmay be drafted to exclude any optional element. As such, this statementis intended to serve as antecedent basis for use of such exclusiveterminology as “solely,” “only” and the like in connection with therecitation of claim elements, or use of a “negative” limitation.

It is appreciated that certain features of the invention, which are, forclarity, described in the context of separate embodiments, may also beprovided in combination in a single embodiment. Conversely, variousfeatures of the invention, which are, for brevity, described in thecontext of a single embodiment, may also be provided separately or inany suitable sub-combination.

The publications discussed herein are provided solely for theirdisclosure prior to the filing date of the present application. Nothingherein is to be construed as an admission that the present invention isnot entitled to antedate such publication by virtue of prior invention.Further, the dates of publication provided may be different from theactual publication dates which may need to be independently confirmed.

DETAILED DESCRIPTION

As summarized above, the present disclosure provides a solid phasemethod of preparing oligonucleotides via sequential coupling cyclesincluding the coupling of a dinucleotide dimer to a free 3′terminalgroup (e.g., a 3′-hydroxyl or 3′-amino group) of a growing chain. Ingeneral terms the synthesis proceeds from the 5′-terminal to the3′-terminal of a target oligonucleotide sequence and includes at leastone coupling of a dinucleotide dimer. The dimer may be coupled to thefree 3′ terminal group of a growing chain via any convenient chemistry.In some cases, the dimer is a3′-protected-dinucleotide-5′-phosphoramidite dimer, where thedinucleotide may include any convenient inter-nucleoside linkage. Theoligonucleotide may include one or more phosphoramidate inter-subunitlinkages (e.g., an oxo-phosphoramidate or thiophosphoramidate linkage).

In some embodiments, the oligonucleotide includes a sequence ofnucleoside subunits containing at least one subunit defined by theformula:

where B¹ is a purine, a protected purine, a pyrimidine or a protectedpyrimidine, or an analog thereof; X is O or S; R is selected from thegroup consisting of hydrogen, an alkyl, a substituted alkyl, an aryl, asubstituted aryl, a phosphate protecting group; and R¹³ is selected fromthe group consisting of hydrogen, O—R², and halogen, wherein R² is H, analkyl, a substituted alkyl (e.g., —(CH₂)_(n)W(CH₂)_(m)H, where n isbetween 1-10, m is between 0-10 and W is O, S, or NH) or a hydroxylprotecting group. It is understood that some of the oligonucleotidesincluding a subunit described by the formula above may also exist in asalt form. Such forms in so far as they may exist, are intended to beincluded within the scope of the present disclosure.

The subject methods provide for a reduced number of coupling cyclesrelative to methods involving only nucleoside monomer subunit couplingsand provide for reduced amounts of non-target oligonucleotide productsof the synthesis. The retrosynthetic strategy utilized for preparing atarget oligonucleotide sequence may be selected depending on a varietyof factors, such as the length and sequence of the targetoligonucleotide so as to minimize the amounts of particular non-targetoligonucleotide products of the synthesis.

In some embodiments, the subject methods provide for the preparation ofcompositions that have a reduced amount of one or more (N−x) productsrelative to a target oligonucleotide of interest.

In certain embodiments, any of the compositions described herein thathave a reduced amount of one or more (N−x) products relative to a targetoligonucleotide of interest are unpurified.

As used herein, the term “(N−x) product” (where x is an integer from 1to N−1 and N is the number of nucleoside residues in a targetoligonucleotide), refers to a non-target oligonucleotide produced duringthe subject methods of preparation that lacks x nucleoside residues bycomparison with the sequence of a target oligonucleotide of N residuesin length. The target oligonucleotide is the product which the subjectmethod of preparation is designed to produce. As such, a (N−1) productis a non-target oligonucleotide that lacks any one nucleoside residueout of the sequence of the target oligonucleotide. As such, in somecases, the term “(N−1) product” refers to a variety of non-targetoligonucleotide products, each of which lack one nucleoside residue bycomparison to the sequence of the target oligonucleotide. Similarly, theterm “(N−x) product” refers to a variety of non-target oligonucleotideproducts, each of which lack x nucleoside residues by comparison to thesequence of the target oligonucleotide. For example, a (N−2) product isa non-target oligonucleotide that lacks any two nucleoside residues outof the sequence of the target oligonucleotide. In some cases the xresidues are contiguous to each other relative to the target oligonucleotide sequence. In other cases, the x residues are discontiguous toeach other relative to the target oligo nucleotide sequence. The xnucleoside residues may be lacking from any location of the targetsequence and may be produced from unreacted 3′-terminal groups during acoupling cycle. The (N−x) products of the subject methods may includeone or more further modifications that derive from the subject methodsof synthesis, e.g., a partial deprotection modification, loss of anucleobase (e.g., depurination), capping of a terminal group,derivatization via a synthesis reagent (e.g., phenylacetylation by asulfurization reagent), and the like. A variety of modifiedoligonucleotides are possible depending on the chemistry ofoligonucleotide synthesis and reagent utilized. Unless indicatedotherwise, all such modifications are meant to be encompassed by theterm (N−x) product.

In some embodiments, the subject methods result in the reduction of oneor more non-target products of oligonucleotide synthesis selected from apartially protected product or a partially protected (N−x) product,e.g., an oligonucleotide product including one or more nucleobaseprotecting groups. In the subject oligonucleotide compositions, thetarget oligonucleotide sequence may be more readily isolated or purifiedfrom other oligonucleotide-containing products of the method, e.g.,(N−x) products and products lacking a nucleobase.

Embodiments of the subject methods and compositions are described inmore detail in the sections below.

Methods of Making Oligonucleotides

The present disclosure provides a method of preparing anoligonucleotide. The subject methods may include at least one couplingof a dinucelotide dimer to the free 3′ terminal group of a growingoligonucleotide chain. Any convenient oligonucleotide synthesis methodsand chemistries may be utilized in the subject methods of preparation.Oligonucleotide synthesis chemistries and methods of interest that maybe adapted for use in the subject methods include, but are not limitedto, phosphoramidite, H-phosphonate, phosphodiester, phosphotriester,phosphite triester, and those described by Fearon et al. in U.S. Pat.No. 5,824,793, the disclosure of which is herein incorporated byreference in its entirety. The oligonucleotide components of theinvention compounds may be synthesized by adapting conventionalprotocols for the type of chemistry selected. Methods of interest forthe synthesis of oligonucleotides having N3′→P5′ phosphoramidatechemistries include, but are not limited to, those methods described inMcCurdy et al., (1997) Tetrahedron Letters, 38:207-210 and Pongracz &Gryaznov, (1999) Tetrahedron Letters, 49:7661-7664.

An oligonucleotide of interest may be prepared using the subject methodsvia sequential couplings starting from the 5′-terminal and proceeding tothe 3′-terminal of the target oligonucleotide sequence. The 5′-terminalnucleoside subunit may be attached to any convenient solid support viaan optional linking group or 5′-terminal group. Then, subunit couplingsto the growing oligonucleotide chain may be achieved using either dimerphosphoramidites or monomer phosphoramidites. Alternatively, the5′-terminal dinucleoide subunit may be attached to any convenient solidsupport via an optional linking group or 5 terminal group. Once thefirst subunit (e.g., monomer or dimer subunit) is attached to the solidsupport, the subunit may be deprotected to produce a free, immobilized3′-terminal group. In some cases, the method includes coupling a supportbound 3′-terminal group with a3′-protected-dinucleotide-5′-phosphoramidite dimer. In certainembodiments, the 3′-terminal group is a 3′-hydroxyl group. In certainembodiments, the 3′-terminal group is a 3′-amino group.

In some instances, the method includes the steps of: (a) deprotectingthe protected 3′ amino group of a terminal nucleoside attached to asolid phase support, said deprotecting forming a free 3′ amino group;(b) contacting the free 3′ amino group with a 3′-protectedamino-dinucleotide thiophosphoramidate orphosphoramidite-5′-phosphoramidite dimer in the presence of anucleophilic catalyst to form an internucleoside N3′→P5′ phosphoramiditelinkage; and (c) oxidizing the linkage.

The target oligonucleotide sequence may be synthesized using aretrosynthetic strategy that includes sequentially coupling of bothdimer and monomer subunits to the 3′terminal group of the growingoligonucleotide chain. As such, in some embodiments, the method furtherincludes the steps of: (a) deprotecting the protected 3′ amino group ofa terminal nucleoside attached to a solid phase support, saiddeprotecting forming a free 3′ amino group; (b) contacting the free 3′amino group with a 3′-protected aminonucleoside-5′-phosphoramiditemonomer in the presence of a nucleophilic catalyst to form aninternucleoside N3′→P5′ phosphoramidite linkage; and (c) oxidizing thelinkage to produce a N3′→P5′ phosphoramidate linkage.

As used herein, the term “N3′→P5′ phosphoramidite linkage” refers to thephosphorus (III) intermediate of the N3′→P5′ phosphoramidate linkage. Ingeneral terms, an N3′→P5′ phosphoramidate linkage is formed by oxidizingan N3′→P5′ phosphoramidite linkage to a phosphorus (V) product (e.g., aN3′→P5′ phosphoramidate linkage that may include an oxo (P═O) or a thio(P═S) group). In some cases, the oxidizing step may be described assulfurizing the N3′→P5′ phosphoramidite linkage to produce a N3′→P5′thiophosphoramidate linkage.

As used herein, “N3′→P5′ phosphoramidate”, “P5′→N3′ phosphoramidate” and“phosphoramidate” refer to an internucleosidic subunit linkage describedby the formula:

3′-NH—P(═X)(OR)—O—5′

or a tautomer thereof, wherein the 3′ and 5′ refer to the carbon atomsof the sugar moieties of consecutive nucleosides which are connected byway of the linkage, and wherein R is hydrogen, an alkyl, a substitutedalkyl, an aryl, a substituted aryl, or a phosphate protecting group, andX is a chalcogen, such as oxygen or sulfur. It is understood that, whenR is hydrogen, an alkyl, a substituted alkyl, an aryl, a substitutedaryl, or a phosphate protecting group, some of the internucleosidicsubunit linkages described by the formula above may also exist in a saltform. Such forms in so far as they may exist, are intended to beincluded within the scope of the present disclosure. In some cases, whenX is sulfur, the phosphoramidate may be referred to as athiophosphoramidate. In some cases, when X is oxygen, the“phosphoramidate” may be referred to as an “oxophosphoramidate”. In somecases, when R is a phosphate protecting group it may be an alkyl, analkenyl, an aryl, an aralkyl, a cycloalkyl, or a substituted versionthereof. In some cases, R is a phosphate protecting group containing 10or less carbon atoms. In certain instances, when R is a phosphateprotecting group it is an alkyl having from 1 to 6 carbon atoms; anelectron-withdrawing β-substituted ethyl (e.g., β-trihalomethyl-,β-cyano-, β-sulfo-, or β-nitro-substituted ethyl); anelectron-withdrawing substituted phenyl (e.g., halo-, sulfo-, cyano-, ornitro-, substituted phenyl); or an electron-withdrawing substitutedphenylethyl. In some embodiments, when R is a phosphate protecting groupit is methyl, β-cyanoethyl, or 4-nitrophenylethyl. In certainembodiments, R is hydrogen, methyl, or β-cyanoethyl.Electron-withdrawing substituents of interest include, but are notlimited to, halo, cyano, nitro, sulfo, or mono-, di-, or trihalomethyl,and the like. Halogen atom substituents are usually fluoro, chloro,bromo, or iodo; and in some instances, they are fluoro or chloro.“Electron-withdrawing” denotes the tendency of a substituent to attractvalence electrons of the molecule of which it is a part, i.e. it iselectronegative, e.g. March, Advanced Organic Chemistry, pgs. 16-18(John Wiley, New York, 1985). Guidance for selecting a phosphateprotecting group is provided in Beaucage and Iyer, Tetrahedron 48:2223-2311 (1992). For convenience, nucleotide phosphoramidates aresometimes indicated herein by a subscripted “np” or “pn” for N3′→P5′phosphoramidates and P3′→N5′ phosphoramidates, respectively. Thus,“U_(np)U” is a dinucleotide in which a 3′-aminouridine and a uridine arelinked by an N3′→P5′ phosphoramidate linkage. When the linkage is anoxo-phosphoramidate, the nucleotide oxo-phosphoramidate is sometimesindicated herein by a subscripted “npo” or “opn” for N3′→P5′phosphoramidates and P3′→N5′ phosphoramidates, respectively. Similarly,nucleotide thiophosphoramidates are sometimes indicated herein by asubscripted “nps” or “spn” for N3′→P5′ thiophosphoramidates and P3′→N5′thiophosphoramidates, respectively. Similarly, 2′-fluoro substituentsare indicated by a superscripted “f”. Thus, “U_(f.np)U” is adinucleotide in which the 5′-most 3′-amino-2′-fluorouridine is linked toa uridine by an N3′→P5′ phosphoramidate linkage. A single leadingsubscripted “p” indicates a 5′ monophosphate, and a single trailingsubscripted “n” indicates a 3′-amino group.

In some instances, the internucleoside subunit linkage is described bythe formula:

3′-NH—P(═X)(OR)—O-5′

or a tautomer thereof, wherein the 3′ and 5′ refer to the carbon atomsof the sugar moieties of consecutive nucleosides which are connected byway of the linkage, and where R is hydrogen and X is oxygen or sulfur.It is understood that for any of the oligonucleotides described hereinthat include such an internucleoside linkage, such oligonucleotides mayalso include any convenient salt forms of the linkage. As such, theinternucleoside linkage may be in a salt form that includes anyconvenient counterion.

Any convenient protecting group strategies may be utilized in thesubject methods to protect the base, phosphoramidite, phosphoramidate,5′, 2′ and/or 3′groups. Protecting groups of interest include, but arenot limited to, those protecting groups described by Ohkubo et al., Org.Lett., 2010, 12 (11), pp 2496-2499; and Beaucage and Iyer, Tetrahedron48: 2223-2311 (1992).

As used herein, the term “phosphate protecting group” refers to aprotecting group that may be attached to a phosphorus-containingintersubunit linkage of an oligonucleotide. When present, a phosphateprotecting group may prevent (i.e., block) reaction of thephosphorus-containing linkage at the location where the phosphateprotecting group is attached. Any convenient phosphorus-containingintersubunit linkages (e.g., P(III) and P(V) linkages) may be protectedby the subject phosphate protecting groups, including, but not limitedto, phosphoramidite, oxophosphoramidate, thiophosphoramidate, phosphateester, thiophosphate ester, phosphodiester linkages and the like. Thephosphate protecting group may be attached to an available oxygen atomof the phosphorus-containing intersubunit linkage. Any convenientprotecting groups may be utilized as a phosphate protecting group.Phosphate protecting groups of interest include, but are not limited to,an alkyl, an alkenyl, an aryl, an aralkyl, a cycloalkyl, or asubstituted version thereof, such as an alkyl having from 1 to 6 carbonatoms, such as an electron-withdrawing β-substituted ethyl (e.g.,β-trihalomethyl-, β-cyano-, β-sulfo-, or β-nitro-substituted ethyl); anelectron-withdrawing substituted phenyl (e.g., halo-, sulfo-, cyano-, ornitro-, substituted phenyl); or an electron-withdrawing substitutedphenylethyl, methyl, β-cyanoethyl, or 4-nitrophenylethyl. In certainembodiments, phosphate protecting group is methyl, or β-cyanoethyl.Electron-withdrawing substituents of interest include, but are notlimited to, halo (e.g., chloro or fluoro), cyano, nitro, sulfo, ormono-, di-, or trihalomethyl, and the like.

The 3′-terminal group of the growing oligonucleotide chain may include a3′-hydroxyl, a 3′-amino group or a protected version thereof. Anyconvenient hydroxyl and/or amino protecting groups may be utilized atthe 3′-terminal group during oligonucleotide synthesis. In someembodiments, the 3′terminal group is a protected 3′-amino group and themethod includes deprotecting or removing the protecting group to producea free 3′amino group.

As used herein, the term “free amino group” in reference to the monomersand dimers means an amino group available for reacting with thephosphoramidite group of an incoming monomer or dimer. In someembodiments, a free amino group is a primary amine. After thedeprotection (e.g., detritylation) step, the amino group may be in theform of a salt (e.g., the salt of a conjugate base of the acid used fordetritylation). This salt optionally may be neutralized with a basicsolution such as 2% triethylamine or pyridine in acetonitrile after thedetritylation step.

In some embodiments, the 3′-terminal group is a protected 3′-hydroxylgroup and the method includes deprotecting or removing the protectinggroup to produce a free 3′-hydroxyl group. In some embodiments, the3′-terminal group is a protected 3′-amino group and the method includesdeprotecting or removing the protecting group to produce a free 3′-aminogroup. The protected 3′-amino or 3′-hydroxyl group may be protected witha trityl protecting group. In certain embodiments, the trityl protectinggroup is triphenylmethyl (Tr, Ph₃C—). In certain embodiments, the tritylprotecting group is 4,4′-dimethoxytrityl (DMT).

Deprotection of the 3′-terminal amino or hydroxyl group may be achievedusing any convenient methods. Methods of interest include, but are notlimited to, those methods described by Beaucage and Iyer, Tetrahedron48: 2223-2311 (1992). In some cases, deprotection of the protected 3′amino group of a terminal nucleoside includes detritylation to produce afree 3′terminal group, e.g., acid-catalyzed detritylation.

In general, the dimer or monomer subunit phosphoramidites include aprotected 3′-hydroxyl or 3′-amino group that is the same as the3′terminal group of the terminal nucleoside attached to the solidsupport. 3′-Protection of the incoming subunit phosphoramidites preventsundesirable polymerization of the chain.

Any convenient solid phase supports may be used in the subject methods.Solid supports of interest include, but are not limited to,microparticles made of controlled pore glass (CPG), highly cross-linkedpolystyrene (e.g., NittoPhase HL 400 or GE Primer 350), acryliccopolymers, cellulose, nylon, dextran, latex, polyacrolein, and thelike, such as those disclosed in the following exemplary references:Meth. Enzymol., Section A, pages 11-147, vol. 44 (Academic Press, NewYork, 1976); U.S. Pat. Nos. 4,678,814; 4,413,070; and 4,046; 720; andPon, Chapter 19, in Agrawal, editor, Methods in Molecular Biology, Vol.20, (Humana Press, Totowa, N.J., 1993). Further supports of interestinclude polystyrene beads; polystyrene grafted with polyethylene glycol(e.g., TentaGel™, Rapp Polymere, Tubingen Germany); and the like.Selection of the support characteristics, such as material, porosity,size, shape, and the like, and the type of linking moiety employeddepends on a variety of factors, such as protection groups employed,length of final product, quantity of final product, and the like.Exemplary linking moieties are disclosed in Pon et al, Biotechniques,6:768-775 (1988); Webb, U.S. Pat. No. 4,659,774; Barany et al,International patent application PCT/US91/06103; Brown et al, J. Chem.Soc. Commun., 1989: 891-893; Damha et al, Nucleic Acids Research, 18:3813-3821(1990); Beattie et al, Clinical Chemistry, 39: 719-722 (1993);Maskos and Southern, Nucleic Acids Research, 20: 1679-1684 (1992); andthe like.

In some embodiments, the solid supports that find use in the subjectmethods include CPG and polystyrene grafted with polyethylene glycol andpossessing a terminal amino group (e.g., TentaGel-NH₂™, Rapp Polymere,Tubingen Germany). The aminopropyl group may be used as a spacer betweenCPG and the nucleoside linkage. In some cases, the linkage to the5′-hydroxyl of the first nucleoside is a succinyl group which provides abase-labile ester linkage that may be cleaved after synthesis withaqueous ammonia.

Following deprotection, the support-bound nucleoside is capable ofreacting with a dimer or monomer subunit phosphoramidite to form aninternucleoside linkage. It is understood that the support-boundnucleoside may refer to a single residue attached to a solid support ormay refer to the terminal residue of an oligonucleotide chain that isattached to the support.

Any convenient coupling chemistry, coupling reagents and methods may beutilized in the subject methods. Considerable guidance in makingselections concerning coupling conditions, protecting groups, solidphase supports, linking groups, deprotection reagents, reagents tocleave products from solid phase supports, purification of product, andthe like, in the context of the subject methods can be found inliterature, e.g. Gait, editor, Oligonucleotide Synthesis: A PracticalApproach (IRL Press, Oxford, 1984); Amarnath and Broom, ChemicalReviews, Vol. 77, pgs. 183-217 (1977); Pon et al, Biotechniques, Vol. 6,pgs. 768-775 (1988); Ohtsuka et al, Nucleic Acids Research, Vol. 10,pgs. 6553-6570 (1982); Eckstein, editor Oligonucleotides. and Analogues:A Practical Approach (IRL Press, Oxford, 1991), Greene and Wuts“Protective Groups in Organic Synthesis”, Third edition, Wiley, New York1999, Narang, editor, Synthesis and Applications of DNA and RNA(Academic Press, New York, 1987), Beaucage and Iyer, Tetrahedron 48:2223-2311 (1992), and like references.

The coupling step of the subject methods may be carried out in thetemperature range of −20 to 200 degrees Centigrade. In some instances,the reaction is carried out at ambient temperature (about 15-30 degreesCentigrade). The reaction may be performed by adding a solution of thephosphoramidite dimer or monomer and a solution of an activator (or asolution containing the phosphoramidite dimer or monomer and theactivator) to the reaction vessel containing the free amino group of an(oligo)nucleotide covalently attached to a solid support. Generally,activators of interest include nucleophilic catalysts that displace themore stable phosphoramidite amino group to form a highly reactive (andless stable) intermediate which, in turn, reacts with the free 3′ aminogroup of a solid supported oligonucleotide N3′→P5′ phosphoramidate. Themixture is then mixed by such methods as mechanical vortexing, spargingwith an inert gas, etc. Alternately, the solution(s) of dimer or monomerand activator can be made to flow through a reaction vessel (or column)containing the solid supported (oligo)nucleotide with a free 3′-terminalgroup. The monomer and the activator either can be premixed, mixed inthe valve-block of a suitable synthesizer, mixed in a pre-activationvessel and pre-equilibrated if desired, or they can be added separatelyto the reaction vessel.

Activators of interest that may be utilized in the subject methodsinclude, but are not limited to, tetrazole, 5-(ethylthio)tetrazole,5-(4-nitrophenyl)tetrazole, 5-(2-thiophene) tetrazole, triazole,pyridinium chloride, and the like, e.g. activating agents as describedby Beaucage and Iyer Tetrahedron 48: 2223-2311 (1992); Berner et al,Nucleic Acids Research, 17: 853-864 (1989); Benson, Chem. Rev. 41: 1-61(1947). As used herein, the term “tetrazole activator” refers toactivators which are tetrazole or derivatives of tetrazole. In someembodiments, the activator is tetrazole. Convenient solvents include,but are not limited to, acetonitrile, tetrahydrofuran, methylenechloride, and the like. Care may be exercised to use dry (free fromwater) dimer or monomer, activator, and solvent for the coupling stepand for the solvent used to wash the solid support immediately beforethe coupling step.

After coupling, the unreacted 3′-amino groups of the support-boundgrowing chain of the oligonucleotide may be optionally capped with aconvenient capping agent before the next deprotection step (e.g.,detritylation step) to render them inert to subsequent coupling steps.This capping step may improve the HPLC profile of the preparation tomake purification more facile, and may also improve the overall yield ofproduct. Capping reagents useful in the subject methods includeelectrophilic reagents such as acetic anhydride and isobutyricanhydride, acid chlorides such as adamantyl carbonyl chloride, pivaoylchloride, and the like, isothiocyanates, chloroformates, etc. Alsouseful are phosphoramidites in conjunction with an activator andfollowed by oxidation, and H-phosphonate salts such as triethylammoniumisopropyl-H-phosphonate used in conjunction with an acid chloride suchas pivaoyl chloride or adamantyl carbonyl chloride.

In some embodiments, the method includes oxidizing an internucleosideN3′→P5′ phosphoramidite linkage. As used herein, the terms “oxidize,”“oxidation,” “oxidizing”, and the like, in reference to aphosphorus-containing internucleosidic linkage means a process ortreatment for converting the phosphorus atom of the linkage from aphosphorus (III) form to a phosphorus (V) form. Oxidation of theinternucleotide linkages may be performed at any convenient point in thesynthesis using any convenient methods. In some embodiments, oxidationis performed in a stepwise manner, e.g., during every coupling cycle. Inother embodiments, oxidation of multiple internucleotide linkages isperformed at the end of the synthesis. In some instances, oxidizing aN3′→P5′ phosphoramidite linkage (e.g., using an iodine/water basedoxidizing agent) produces an oxo-phosphoramidate linkage. In otherinstances, oxidizing a N3′→P5′ phosphoramidite linkage includessulfurization to produce a thiophosphoramidate linkage. Sulfurizationmay be performed using any convenient methods. Sulfurization methods ofinterest include those described by Gryazonov et al., WO2001018015, thedisclosure of which is herein incorporated by reference in its entirety.Sulfurizing agents for use in the invention include elemental sulfur,thiuram disulfides such as tetraethyl thiuram disulfide, acyl disulfidessuch as phenacyldisulfide, phosphinothioyl disulfides such as S-Tetra™,and 1,1-dioxo-3H-1,2-benzodithiol-3-one. In some embodiments,sulfurization may be performed using elemental sulfur (S8). In certainembodiments, sulfurization may be performed using Beaucage reagent,using methods as described by Iyer et al., J. Organic Chemistry55:4693-4699, 1990.

Oxidizing agents which are useful in the method include iodine,chlorine, bromine, peracids such as m-chlorobenzoic acid, hydroperoxidessuch as t-butylhydroperoxide, ethyl hydroperoxide, methyl hydroperoxideand the like, ozone, mixed acyl-sulfinic anhydrides such as3H-2,1-benzoxathiolan-3-one-1-oxide, salts of persulfates such assodium, ammonium, and tetrabutylammonium persulfate and the like,monoperoxysulfates such as oxone™, sodium and/or other hypochlorites,peroxides such as diethyl peroxide or bis(trimethylsilyl)peroxide, orhydrogen peroxide or non aqueous hydrogen peroxide equivalents such asurea/hydrogen peroxide complex, etc. Other useful oxidizing agents whichmay be used to convert phosphorus (III) to phosphorus (V) are describedin Beaucage and Iyer Tetrahedron 48: 2223-2311 (1992).

In some cases, the oxidizing or sulfurizing agent may have a tendency toundergo an undesired Arbuzov side reaction in parallel with the desiredoxidation (Beaucage and Iyer, cited above). The Arbuzov side reactioncan lead to a deprotected phosphoramidate which is unstable to theacidic conditions of subsequent detritylation steps, and result inoligonucleotide fragmentation. In certain embodiments, hydrogen peroxideis used as the oxidizing agent to minimize the Arbuzov side reaction. Incertain embodiments, oxidation includes contacting the oligonucleotidewith a solution of 1.5% hydrogen peroxide, 3.5% water, 20% pyridine, and75% THF.

In some embodiments, the method includes the steps of:

(a) deprotecting a protected 3′ amino group of a terminal nucleosideattached to a solid phase support, said deprotecting forming a free 3′amino group;

(b) reacting the free 3′ amino group with either:

-   -   (i) a 3′-protected amino-dinucleotide        phosphoramidate-5′-phosphoramidite dimer; or    -   (ii) a 3′-protected aminonucleoside-5′-phosphoramidite monomer;        in the presence of a nucleophilic catalyst to form an        internucleoside N3′→P5′ phosphoramidite linkage;

(c) oxidizing the linkage; and

(d) repeating steps (a) through (c) until the polynucleotide issynthesized, wherein the repeating steps (a) through (c) comprisesperforming step (b)(i) at least once.

In some embodiments, the repeating steps (a) through (c) comprisesperforming step (b)(i) twice or more. In certain embodiments, therepeating steps (a) through (c) comprises performing step (b)(i) 3 timesor more, such as 4 times or more, 5 times or more, 6 times or more, 7times or more, 8 times or more, 9 times or more, 10 times or more, 15times or more, 20 times or more, or even 30 times or more. In certainembodiments, the repeating steps (a) through (c) comprises performingstep (b)(i) at every coupling step. In certain embodiments, therepeating steps (a) through (c) comprises performing step (b)(i) atevery coupling step except one. In certain embodiments, the repeatingsteps (a) through (c) comprises performing step (b)(ii) once and onlyonce. In certain embodiments, the repeating steps (a) through (c)comprises performing step (b)(ii) twice and only twice.

As described herein, it is understood that the term phosphoramidatelinkage is meant to encompass both oxo-phosphoramidate andthiophosphoramidate linkages (e.g., as depicted in Formula I). Incertain embodiments of the method, oxidizing the internucleoside N3′→P5′phosphoramidite linkage produces an oxo-phosphoramidate linkage. In someembodiments of the method, oxidizing the internucleoside N3′→P5′phosphoramidite linkage includes sulfurization to produce athiophosphoramidate linkage.

In some embodiments of the method, the oligonucleotide is described byFormula (I):

wherein:

-   -   each B¹ is independently a purine, a protected purine, a        pyrimidine or a protected pyrimidine, or an analog thereof;    -   each X is independently oxygen or sulfur;    -   each R¹³ is hydrogen, fluoro, hydroxyl, an alkoxy, a substituted        alkoxy or a protected hydroxyl;    -   R⁶ is amino, hydroxyl, a protected amino, a protected hydroxy,        —O-L-Z or —NH-L-Z;    -   each L is independently an optional linker;    -   each Z is independently H, a lipid, a support, a carrier, an        oligonucleotide, a polymer, a polypeptide, a detectable label,        or a tag;    -   R is hydrogen, an alkyl, a substituted alkyl, an aryl, a        substituted aryl or a phosphate protecting group; and    -   n is an integer of 1 to 1000. When R is hydrogen, an alkyl, a        substituted alkyl, an aryl, a substituted aryl or a phosphate        protecting group, it is understood that some of the        oligonucleotides of Formula (I), may also exist in a salt form.        Such forms in so far as they may exist, are intended to be        included within the scope of the present disclosure.

In some embodiments of Formula (I), each R¹³ is hydrogen. In someembodiments of Formula (I), each R¹³ is fluoro. In some embodiments ofFormula (I), each R¹³ is hydroxyl.

In some embodiments of Formula (I), R⁶ is amino. In certain embodimentsof Formula (I), R⁶ is hydroxyl.

In some embodiments of Formula (I), each R is hydrogen. It is understoodthat when R is hydrogen, the phosphate linkage may be charged underaqueous conditions, such as physiological conditions. As such, it isunderstood that oligonucleotides of Formula (I) may also include anyconvenient salt forms of the linkage. As such, the internucleosidelinkage of Formula (I) may be in a salt form that includes anyconvenient counterion. In some embodiments of Formula (I), each R is analkyl or a substituted alkyl. In some embodiments of Formula (I), each Ris an aryl or a substituted aryl. In some embodiments of Formula (I),each R is a phosphate protecting group.

In some embodiments of Formula (I), Z is H. In some embodiments ofFormula (I), Z is a lipid (e.g., as described herein). In certain cases,the lipid is a fatty acid (e.g., as described herein). In someembodiments of Formula (I), Z is a support. In some embodiments ofFormula (I), Z is a carrier. In some embodiments of Formula (I), Z is anoligonucleotide. In some embodiments of Formula (I), Z is a polymer. Incertain cases, the polymer is a PEG. In some embodiments of Formula (I),Z is a polypeptide. In some embodiments of Formula (I), Z is adetectable label. In some embodiments of Formula (I), Z is a tag.

In some embodiments of Formula (I), L is absent.

In some embodiments, each B¹ is independently selected from A, C, G, Tand U or a protected version thereof.

In certain embodiments of Formula (I), n is an integer of between 1 and500, such as between 1 and 100, between 1 and 75, between 1 and 50,between 1 and 40, between 1 and 30, between 1 and 20, between 1 and 15,between 1 and 10, or between 4 and 10. In certain embodiments, n is aninteger of between 1 and 100, such as between 5 and 50, between 10 and50, between 10 and 40, between 10 and 30, between 10 and 25, between 10and 20, between 12 and 18, or between 12 and 16. In certain embodiments,n is 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21,22, 23, 24 or 25.

In certain embodiments of the method, the oligonucleotide comprises asequence of nucleoside subunits complementary to the RNA component ofhuman telomerase, and wherein at least two of the nucleoside subunitsare joined by a N3′→P5′ phosphoramidate inter-subunit linkage.

In some embodiments of the method, the oligonucleotide includes asequence of between 3 and 50 nucleoside contiguous subunitscomplementary to the RNA component of human telomerase, such as between5 and 40, between 10 and 40, between 10 and 30, between 10 and 25,between 10 and 20, between 12 and 18, or between 12 and 16 nucleosidesubunits. In certain embodiments, the oligonucleotide includes asequence of 10 or more contiguous nucleoside subunits complementary tothe RNA component of human telomerase. In certain embodiments, theoligonucleotide includes a sequence of 7 or more contiguous nucleosidesubunits, such as 7, 8, 9, 10, 11, 12, 13, 14, 15, 16 or 17 contiguousnucleoside subunits. In certain embodiments, the oligonucleotideincludes a sequence of between 11 and 18, such as between 11 and 16contiguous nucleoside subunits complementary to the RNA component ofhuman telomerase.

In some instances of the method, the N3′→P5′ thiophosphoramidateinter-subunit linkage is described by the following structure:

3′-NH—P(S)(OR)—O-5′

where R is selected from the group consisting of hydrogen, an alkyl, asubstituted alkyl, an aryl, a substituted aryl and a phosphateprotecting group. It is understood that, when R is selected from thegroup consisting of hydrogen, an alkyl, a substituted alkyl, an aryl, asubstituted aryl and a phosphate protecting group, some of theinternucleoside subunit linkages described by the formula above may alsoexist in a salt form. Such forms in so far as they may exist, areintended to be included within the scope of the present disclosure.

In some instances of the method, the N3′→P5′ thiophosphoramidateinter-subunit linkage is described by the following structure:

3′-NH—P(S)(OR)—O-5′

where R is hydrogen. It is understood that for any of theoligonucleotides described herein that includes such an inter-subunitlinkage, such oligonucleotides may also include any convenient saltforms of the linkage. As such, the inter-subunit linkage may be in asalt form that includes any convenient counterion.

In some embodiments of the method, the oligonucleotide includes thesequence TAGGGTTAGACAA (SEQ ID NO:3). In certain embodiments, all of theinternucleotide inter-subunit linkages of the TAGGGTTAGACAA (SEQ IDNO:3) sequence are N3′→P5′ phosphoramidate inter-subunit linkages. Incertain instances, all of the N3′→P5′ phosphoramidate inter-subunitlinkages of the sequence are N3′→P5′ thiophosphoramidate inter-subunitlinkages (e.g., nps linkages). In certain instances, all of the N3′→P5′phosphoramidate inter-subunit linkages of the sequence are N3′→P5′oxo-phosphoramidate inter-subunit linkages (e.g., np linkages).

In some embodiments of the method, the polynucleotide includes a3′-amino or a 3′-hydroxyl terminal group. In certain embodiments of themethod, the polynucleotide includes a 3′-amino terminal group. Incertain embodiments of the method, the polynucleotide includes a3′-hydroxyl terminal group.

In some embodiments of the method, the oligonucleotide is described bythe structure:

where “nps” represents a thiophosphoramidate linkage (e.g.,—NH—P(═O)(SH)—O— or a tautomer thereof), connecting the 3′-carbon of onenucleoside to the 5′-carbon of the adjacent nucleoside.

It is understood that all embodiments referring to an oligonucleotideare also applicable to the salt forms of said oligonucleotide.

In some embodiments of the method, the oligonucleotide is described bythe structure:

or a salt thereof;where “nps” represents a thiophosphoramidate linkage (e.g.,—NH—P(═O)(SH)—O— or a tautomer thereof, or a salt thereof), connectingthe 3′-carbon of one nucleoside to the 5′-carbon of the adjacentnucleoside. In certain embodiments, the composition includes apharmaceutically acceptable salt of the compound. In certain instances,the composition includes a sodium salt of the compound. In certainembodiments, the composition includes a divalent cation salt of thecompound, such as a magnesium salt of the compound. In certainembodiments, the composition includes a trivalent cation salt of thecompound, such as an aluminium salt of the compound.

In certain embodiments of the method, the oligonucleotide is describedby the following structure, where each M^(x+) is independently hydrogenor any convenient counterion of a salt, each x is independently 1, 2 or3 and n is an integer from 5 to 13, such as 5, 6, 7, 8, 9, 10, 11, 12 or13, such as n is 13:

In certain instances, each x is 1. In certain instances, each x isindependently 1 or 2. In certain instances, each x is independently 1 or3. In certain instances, M^(x+) is hydrogen.

In certain embodiments of the method, the oligonucleotide is describedby the following structure and may include any convenient cationiccounterions of a salt:

In certain embodiments of the method, the oligonucleotide is describedby the structure:

In certain embodiments of the method, the C11 nucleotide residue of theTAGGGTTAGACAA (SEQ ID NO:3) sequence derives from a 3′-protectedaminonucleoside-5′-phosphoramidite monomer. By “derives from” is meantthat the residue of interest is introduced during synthesis via aparticular subunit. In certain instances, the T1 to A10, A12 and A13residues of the TAGGGTTAGACAA (SEQ ID NO:3) sequence derive from3′-protected amino-dinucleotide thiophosphoramidate-5′-phosphoramiditedimers.

In some cases, the method includes sequential coupling of the following3′-protected amino-dinucleotide thiophosphoramidate-5′-phosphoramiditedimers and 3′-protected aminonucleoside-5′-phosphoramidite monomer to aterminal group of a solid phase support: TA, GG, GT, TA, GA, C and AA.It is understood that for simplicity, a protected phosphoramiditesubunit that finds use in couplings of the subject methods may bedepicted via the symbols X¹ or X¹X², where X¹ and X² are independentlyany convenient nucleosides linked via any convenient internucleosidelinkage (e.g., as described herein). Any convenient synthetic strategiesmay be utilized in the subject methods. Some strategies of interest areshown below to demonstrate how the preparation of an oligonucleotidetarget sequence may be allocated to particular dimer and/or monomersubunits.

Exemplary retrosynthetic strategies represented by the following listsof sequential dimer and/or monomer subunits are provided for anexemplary target oligonucleotide sequence TAGGGTTAGACAA (SEQ ID NO:3).It is understood that this list of strategies is not exhaustive, and maybe adapted for application to any convenient target oligonucleotidesynthesis. In some embodiments, the method includes sequential couplingof one of the following series of 3′-protected amino-dinucleotidethiophosphoramidate-5′-phosphoramidite dimers and/or 3′-protectedaminonucleoside-5′-phosphoramidite monomers to a terminal group of asolid phase support:

TA, G, G, G, T, T, A, G, A, C, A, A

T, AG, G, G, T, T, A, G, A, C, A, A

T, A, GG, G, T, T, A, G, A, C, A, A

T, A, G, GG, T, T, A, G, A, C, A, A

T, A, G, G, GT, T, A, G, A, C, A, A

T, A, G, G, G, TT, A, G, A, C, A, A

T, A, G, G, G, T, TA, G, A, C, A, A

T, A, G, G, G, T, T, AG, A, C, A, A

T, A, G, G, G, T, T, A, GA, C, A, A

T, A, G, G, G, T, T, A, G, AC, A, A

T, A, G, G, G, T, T, A, G, A, CA, A

T, A, G, G, G, T, T, A, G, A, C, AA

TA, GG, G, T, T, A, G, A, C, A, A

TA, G, GG, T, T, A, G, A, C, A, A

TA, G, G, GT, T, A, G, A, C, A, A

TA, G, G, G, TT, A, G, A, C, A, A

TA, G, G, G, T, TA, G, A, C, A, A

TA, G, G, G, T, T, AG, A, C, A, A

TA, G, G, G, T, T, A, GA, C, A, A

TA, G, G, G, T, T, A, G, AC, A, A

TA, G, G, G, T, T, A, G, A, CA, A

TA, G, G, G, T, T, A, G, A, C, AA

T, AG, GG, T, T, A, G, A, C, A, A

T, AG, G, GT, T, A, G, A, C, A, A

T, AG, G, G, TT, A, G, A, C, A, A

T, AG, G, G, T, TA, G, A, C, A, A

T, AG, G, G, T, T, AG, A, C, A, A

T, AG, G, G, T, T, A, GA, C, A, A

T, AG, G, G, T, T, A, G, AC, A, A

T, AG, G, G, T, T, A, G, A, CA, A

T, AG, G, G, T, T, A, G, A, C, AA

T, A, GG, GT, T, A, G, A, C, A, A

T, A, GG, G, TT, A, G, A, C, A, A

T, A, GG, G, T, TA, G, A, C, A, A

T, A, GG, G, T, T, AG, A, C, A, A

T, A, GG, G, T, T, A, GA, C, A, A

T, A, GG, G, T, T, A, G, AC, A, A

T, A, GG, G, T, T, A, G, A, CA, A

T, A, GG, G, T, T, A, G, A, C, AA

T, A, G, GG, TT, A, G, A, C, A, A

T, A, G, GG, T, TA, G, A, C, A, A

T, A, G, GG, T, T, AG, A, C, A, A

T, A, G, GG, T, T, A, GA, C, A, A

T, A, G, GG, T, T, A, G, AC, A, A

T, A, G, GG, T, T, A, G, A, CA, A

T, A, G, GG, T, T, A, G, A, C, AA

T, A, G, G, GT, TA, G, A, C, A, A

T, A, G, G, GT, T, AG, A, C, A, A

T, A, G, G, GT, T, A, GA, C, A, A

T, A, G, G, GT, T, A, G, AC, A, A

T, A, G, G, GT, T, A, G, A, CA, A

T, A, G, G, GT, T, A, G, A, C, AA

T, A, G, G, G, TT, AG, A, C, A, A

T, A, G, G, G, TT, A, GA, C, A, A

T, A, G, G, G, TT, A, G, AC, A, A

T, A, G, G, G, TT, A, G, A, CA, A

T, A, G, G, G, TT, A, G, A, C, AA

T, A, G, G, G, T, TA, GA, C, A, A

T, A, G, G, G, T, TA, G, AC, A, A

T, A, G, G, G, T, TA, G, A, CA, A

T, A, G, G, G, T, TA, G, A, C, AA

T, A, G, G, G, T, T, AG, AC, A, A

T, A, G, G, G, T, T, AG, A, CA, A

T, A, G, G, G, T, T, AG, A, C, AA

T, A, G, G, G, T, T, A, GA, CA, A

T, A, G, G, G, T, T, A, GA, C, AA

TA, GG, GT, T, A, G, A, C, A, A

TA, GG, G, TT, A, G, A, C, A, A

TA, GG, G, T, TA, G, A, C, A, A

TA, GG, G, T, T, AG, A, C, A, A

TA, GG, G, T, T, A, GA, C, A, A

TA, GG, G, T, T, A, G, AC, A, A

TA, GG, G, T, T, A, G, A, CA, A

TA, GG, G, T, T, A, G, A, C, AA

TA, G, GG, TT, A, G, A, C, A, A

TA, G, GG, T, TA, G, A, C, A, A

TA, G, GG, T, T, AG, A, C, A, A

TA, G, GG, T, T, A, GA, C, A, A

TA, G, GG, T, T, A, G, AC, A, A

TA, G, GG, T, T, A, G, A, CA, A

TA, G, GG, T, T, A, G, A, C, AA, etc.

TA, GG, GT, TA, G, A, C, A, A

TA, GG, GT, T, AG, A, C, A, A

TA, GG, GT, T, A, GA, C, A, A

TA, GG, GT, T, A, G, AC, A, A

TA, GG, GT, T, A, G, A, CA, A

TA, GG, GT, T, A, G, A, C, AA, etc

TA, GG, GT, TA, GA, C, A, A

TA, GG, GT, TA, G, AC, A, A

TA, GG, GT, TA, G, A, CA, A

TA, GG, GT, TA, G, A, C, AA, etc

TA, G, GG, TT, AG, AC, A, A

TA, G, GG, TT, AG, A, CA, A

TA, G, GG, TT, AG, A, C, AA

TA, G, G, GT, TA, GA, CA, A

TA, G, G, GT, TA, GA, C, AA

TA, G, G, GT, TA, GA, CA, A

TA, G, G, G, TT, AG, AC, AA

TA, G, GG, T, TA, GA, CA, A

TA, G, GG, T, TA, GA, C, AA

TA, G, GG, T, TA, G, AC, AA, etc

T, A, G, GG, TT, AG, AC, AA

T, A, GG, G, TT, AG, AC, AA

T, AG, G, G, TT, AG, AC, AA

TA, G, G, G, TT, AG, AC, AA

T, AG, G, GT, T, AG, AC, AA, etc

T, AG, GG, T, T, AG, AC, AA, etc

T, AG, GG, TT, A, G, AC, AA, etc

T, AG, GG, TT, AG, A, C, AA, etc

T, AG, GG, TT, AG, AC, A, A

T, AG, GG, TT, AG, AC, AA

TA, G, GG, TT, AG, AC, AA

TA, GG, G, TT, AG, AC, AA

TA, GG, GT, T, AG, AC, AA

TA, GG, GT, TA, G, AC, AA

TA, GG, GT, TA, GA, C, AA or

TA, GG, GT, TA, GA, CA, A.

In some embodiments, the method includes sequential coupling of a seriesof 3′-protected amino-dinucleotidethiophosphoramidate-5′-phosphoramidite dimers and/or 3′-protectedaminonucleoside-5′-phosphoramidite monomers to a terminal group of asolid phase support, where at least the final coupling of the synthesisis a dimer coupling. In certain embodiments, the second-to-last couplingand the final coupling are dimer couplings. In certain cases, when N iseven, the method includes N/2 dimer couplings. In certain instances,when N is even, the method includes N/2-1 dimer couplings. In certaininstances, when N is even, the method includes N/2-2 dimer couplings. Incertain instances, when N is even, the method includes N/2-3 dimercouplings. In certain instances, when N is even, the method includesN/2-4 dimer couplings. In certain instances, when N is even, the methodincludes N/2-5 dimer couplings. In certain cases, when N is odd, themethod includes N/2-1 dimer couplings. In certain instances, when N isodd, the method includes N/2-2 dimer couplings. In certain instances,when N is odd, the method includes N/2-3 dimer couplings. In certaininstances, when N is odd, the method includes N/2-4 dimer couplings. Incertain instances, when N is odd, the method includes N/2-5 dimercouplings. In certain instances, when N is odd, the method includesN/2-6 dimer couplings. For example, a sequential coupling of thefollowing series of 3′-protected amino-dinucleotidethiophosphoramidate-5′-phosphoramidite dimers and/or 3′-protectedaminonucleoside-5′-phosphoramidite monomers to a terminal group of asolid phase support:

T, A, G, G, G, T, T, A, G, A, C, AA

T, A, G, G, G, T, T, A, G, AC, AA

T, A, G, G, G, T, T, A, GA, C, AA

T, A, G, G, G, T, T, AG, A, C, AA

T, A, G, G, G, T, TA, G, A, C, AA

T, A, G, G, G, TT, A, G, A, C, AA

T, A, G, G, GT, T, A, G, A, C, AA

T, A, G, GG, T, T, A, G, A, C, AA

T, A, GG, G, T, T, A, G, A, C, AA

T, AG, G, G, T, T, A, G, A, C, AA

TA, G, G, G, T, T, A, G, A, C, AA, etc

T, A, G, G, G, T, T, AG, AC, AA

T, A, G, G, G, TT, AG, AC, AA

T, A, G, GG, TT, AG, AC, AA

T, AG, GG, TT, AG, AC, AA

TA, G, GG, TT, AG, AC, AA

TA, GG, G, TT, AG, AC, AA

TA, GG, GT, T, AG, AC, AA

TA, GG, GT, TA, G, AC, AA

TA, GG, GT, TA, GA, C, AA.

In some embodiments of the method, the 3′-protected amino-dinucleotidethiophosphoramidate-5′-phosphoramidite dimer is described by the formulaX¹X², where X and X² are independently selected from a protectedadenine, a protected cytosine, a protected guanine, thymine and uracil.

Lipid Modified Oligonucleotides

A variety of synthetic approaches can be used to conjugate a lipidmoiety L′ to the oligonucleotide, depending on the nature of the linkageselected, including the approaches described in Mishra et al., (1995)Biochemica et Biophysica Acta, 1264:229-237, Shea et al., (1990) NucleicAcids Res. 18:3777-3783, and Rump et al., (1998) Bioconj. Chem.9:341-349. The synthesis of compounds in which the lipid moiety isconjugated at the 5′ or 3′ terminus of the oligonucleotide can beachieved through use of suitable functional groups at the appropriateterminus, in some cases an amino group, which can be reacted withcarboxylic acids, acid chlorides, anhydrides and active esters. Thiolgroups may also be used as functional groups (see Kupihar et al., (2001)Bioorganic and Medicinal Chemistry 9:1241-1247). Both amino- andthiol-modifiers of different chain lengths are commercially availablefor oligonucleotide synthesis. Oligonucleotides having N3′→P5′phosphoramidate (e.g., N3′→P5′ thiophosphoramidate) linkages contain3′-amino groups (rather than 3′-hydroxy found in most conventionaloligonucleotide chemistries), and hence these oligonucleotides provide aunique opportunity for conjugating lipid groups to the 3′-end of theoligonucleotide.

Various approaches can be used to attach lipid groups to the termini ofoligonucleotides with the N3′→P5′ phosphoramidate (e.g., N3′→P5′thiophosphoramidate) chemistry (see e.g.,3-palmitoylamido-1-O-(4,4′-dimethoxytrityl)-2-O-succinyl propanediollinker of Table 2). For attachment to the 3′ terminus, the conjugatedcompounds can be synthesized by reacting the free 3′-amino group of thefully protected solid support bound oligonucleotide with thecorresponding acid anhydride followed by deprotection with ammonia andpurification. Alternatively, coupling of carboxylic acids of lipids tothe free 3′-amino group of the support bound oligonucleotide usingcoupling agents such as carbodiimides, HBTU or2-chloro-1-methylpyridinium iodide can be used to conjugate the lipidgroups. These two methods form an amide bond between the lipid and theoligonucleotide. Lipids may also be attached to the oligonucleotidechain using a phosphoramidite derivative of the lipid coupled to theoligonucleotides during chain elongation. This approach yields aphosphoramidate (e.g., thiophosphoramidate) linkage connecting the lipidand the oligonucleotide (exemplified by propyl-palmitoyl and2-hydroxy-propyl-palmitoyl compounds). Still another approach involvesreaction of the free 3′-amino group of the fully protected support boundoligonucleotide with a suitable lipid aldehyde, followed by reductionwith sodium cyanoborohydride, which produces an amine linkage.

For attachment to the 5′ terminus, the oligonucleotide can besynthesized using a modified, lipid-containing solid support, followedby synthesis of the oligonucleotide in the 5′ to 3′ direction asdescribed in Pongracz & Gryaznov (1999). An example of the modifiedsupport is provided below. In the instance where n=14, the fatty acid ispalmitic acid: reaction of 3-amino-1,2-propanediol with palmitoylchloride, followed by dimethoxytritylation and succinylation providedthe intermediate used for coupling to the solid support. R may be longchain alkyl amine controlled pore glass.

Dimers Useful for Making Oligonucleotides

In some embodiments of the method of making an oligonucleotide, themethod includes contacting a support-bound free 3′-terminal group (e.g.,a 3′-hydroxyl or 3′-amino group) with a dinucleotide dimer subunit toform an inter-subunit linkage. In general, the dinucleotide dimer is3′-protected and includes a 5′-group capable of coupling with the3′-terminal group. In some embodiments, the dinucleotide dimer includesa 5′-phosphoramidite. The dinucleotide dimer may include a 3′-protectedamino group or a 3′-protected hydroxyl group. In some embodiments, thedinucleotide is described by the formula X¹X², where X¹ and X² areindependently any convenient nucleosides (e.g., A, C, G, T or U or aprotected version thereof) linked via any convenient internucleosidelinkage (e.g., as described herein). The dinucleotide may include anyconvenient internucleoside linkage between the two nucleosides.Internucleoside linkages of interest that find use in the dinucleotidedimers include, but are not limited to, a phosphodiester, aphosphotriester, a methylphosphonate, a phosphoramidate (e.g., athiophosphoramidate) and a phosphorothioate linkage.

In some cases, the dinucleotide dimer is a3′-protected-dinucleotide-5′-phosphoramidite dimer, or a syntheticprecursor thereof, where the dinucleotide is described by the formulaX¹X², where X¹ and X² are independently selected from A, C, G, T and Uor a protected version thereof, and where X¹ and X² are linked via aphosphodiester, a phosphotriester, a methylphosphonate, aphosphoramidate (e.g., a thiophosphoramidate) or a phosphorothioatelinkage, or a protected version thereof.

In some embodiments of the method of making an oligonucleotide, themethod includes contacting a support-bound free 3′-amino group with a3′-protected amino-dinucleotide phosphoramidate-5′-phosphoramidite dimerto form an internucleoside N3′→P5′ phosphoramidite linkage. Anyconvenient 3′-protected amino-dinucleotidephosphoramidate-5′-phosphoramidite dimer, or synthetic precursorsthereof, may find use in the subject methods. In some cases, the dimermay be represented by the one of the following sequences: AA, AC, AG,AT, AU, CA, CC, CG, CT or CU, GA, GC, GG, GT or GU, TA or UA, TC or UC,TG or UG and TT or UU. In some cases, the dimer includes protected2′-hydroxyl groups.

In certain embodiments, the dinucleotide dimer is a dinucleotidethiophosphoramidate compound described by Formula (II):

wherein B¹ and B² are each independently a purine, a protected purine, apyrimidine or a protected pyrimidine, or an analog thereof; R¹¹ ishydrogen, a protecting group or a phosphoramidite group; R¹² is hydrogenor a protecting group; and R¹³ is hydrogen, an alkyl, a substitutedalkyl, an aryl, a substituted aryl or a protecting group. In some cases,B¹ and/or B² include a nucleobase protecting group. It is understoodthat, when R¹³ is hydrogen, an alkyl, a substituted alkyl, an aryl, asubstituted aryl or a protecting group, some of the dinucleotide dimersdescribed by Formula (II) may also exist in a salt form. Such forms inso far as they may exist, are intended to be included within the scopeof the present disclosure.

In some embodiments of Formula (II), R¹¹ is hydrogen. In someembodiments of Formula (II), R¹¹ is a protecting group. Any convenientprotecting groups may find use in the subject dimers of Formula (II). Insome embodiments of Formula (II), R¹¹ is a levulinate-based protectinggroup. In some embodiments of Formula (II), R¹¹ is a levulinateprotecting group (i.e., —COCH₂CH₂COCH₃). In some embodiments of Formula(II), R¹¹ is a 5′-phosphoramidite group.

In some embodiments of Formula (II), R¹² is hydrogen. In someembodiments of Formula (II), R¹² is a protecting group. In certainembodiments, R¹² is a trityl group (e.g., a triphenylmethyl (Trt), amonomethoxytrityl (MMT), or a dimethoxytrityl (DMT)). In someembodiments of Formula (II), R¹² is a Trt protecting group.

In some embodiments of Formula (II), R¹² is a photocleavable protectinggroup. Any convenient photocleavable protecting groups may find use inthe preparation of the subject dinucleotide dimers and syntheticprecursors thereof. In some embodiments of Formula (II), R¹² is asubstituted pixyl protecting group, such as a nitro, fluoro, methyl,trifluoromethyl, and/or methoxy-substituted pixyl protecting group. Insome embodiments of Formula (II), R¹² is a pixyl protecting group (i.e.,a 9-(9-phenyl)xanthenyl).

In some embodiments of Formula (II), R¹¹ is a levunyl protecting groupand R¹² is a trityl protecting group.

In some embodiments of Formula (II), R¹³ is hydrogen. In someembodiments of Formula (II), R¹³ is a protecting group. In certainembodiments, R¹³ is a 2-cyano-ethyl group.

In certain embodiments, the 3′-protected amino-dinucleotidephosphoramidate-5′-phosphoramidite dimer is described by Formula (III):

wherein B¹ and B² are each independently a purine, a protected purine, apyrimidine or a protected pyrimidine, or an analog thereof. In somecases, B¹ and/or B² include a nucleobase protecting group.

In certain embodiments, the 3′-protected amino-dinucleotidephosphoramidate-5′-phosphoramidite dimer is described by Formula (III):

wherein B¹ and B² are each independently a purine, a protected purine, apyrimidine or a protected pyrimidine, or an analog thereof; and R¹⁸ is atrityl protecting group (such as a Trt, a DMT or a MMT) or a pixylprotecting group.

In some embodiments of Formulae (II) or (III), B¹ and B² are eachindependently selected from a protected adenine, a protected cytosine, aprotected guanine, thymine and uracil. In some embodiments of Formulae(II) or (III), B¹ and B² are each independently selected from A(Bz),A(DMF), C(Bz), G(isobutyryl), T and U. In some embodiments of Formulae(II) or (III), B¹ is A(Bz). In some embodiments of Formulae (II) or(III), B¹ is A(DMF). In some embodiments of Formulae (II) or (III), B¹is C(Bz). In some embodiments of Formulae (II) or (III), B¹ isG(isobutyryl). In some embodiments of Formulae (II) or (III), B¹ is T orU. In some embodiments of Formulae (II) or (III), B² is A(Bz) or A(DMF).In some embodiments of Formulae (II) or (III), B² is C(Bz). In someembodiments of Formulae (II) or (III), B² is G(isobutyryl). In someembodiments of Formulae (II) or (III), B² is T or U.

In some embodiments of Formulae (II) or (III), B¹ is A(Bz) or A(DMF) andB² is A(Bz) or A(DMF). In some embodiments of Formulae (II) or (III), B¹is A(Bz) or A(DMF) and B² is C(Bz). In some embodiments of Formulae (II)or (III), B¹ is A(Bz) or A(DMF) and B² is G(isobutyryl). In someembodiments of Formulae (II) or (III), B¹ is A(Bz) or A(DMF) and B² is Tor U.

In some embodiments of Formulae (II) or (III), B¹ is C(Bz) and B² isA(Bz) or A(DMF). In some embodiments of Formulae (II) or (III), B¹ isC(Bz) and B² is C(Bz). In some embodiments of Formulae (II) or (III), B¹is C(Bz) and B² is G(isobutyryl). In some embodiments of Formulae (II)or (III), B¹ is C(Bz) and B² is T or U.

In some embodiments of Formulae (II) or (III), B¹ is G(isobutyryl) andB² is A(Bz) or A(DMF). In some embodiments of Formulae (II) or (III), B¹is G(isobutyryl) and B² is C(Bz). In some embodiments of Formulae (II)or (III), B¹ is G(isobutyryl) and B² is G(isobutyryl). In someembodiments of Formulae (II) or (III), B¹ is G(isobutyryl) and B² is Tor U.

In some embodiments of Formulae (II) or (III), B¹ is T or U and B² isA(Bz) or A(DMF). In some embodiments of Formulae (II) or (III), B¹ is Tor U and B² is C(Bz). In some embodiments of Formulae (II) or (III), B¹is T or U and B² is G(isobutyryl). In some embodiments of Formulae (II)or (III), B¹ is T or U and B² is T or U. It is understood that any ofthe embodiments of Formulae (II) or (III) described herein, can also beapplied to Formula (IV).

Any of the dimers described herein may be adapted for use in the subjectmethods. The subject dimers may be prepared according to any convenientmethods from any convenient nucleoside monomers. Nucleoside monomers ofinterest that find use in the preparation of the subject nucleosidedimers include, but are not limited to, monomers 16, 17, 12 and 13 whichare depicted in the synthetic schemes disclosed herein. Dinucleotidedimers of interest include non-phosphitylated dimers that find use inthe preparation of the subject phosphitylated dinucleotide dimers, suchas dimers 18 and 19 which find use in the preparation of phosphitylateddinucleotide dimers such as 20, or dimer 14 which finds use in thepreparation of phosphitylated dinucleotide dimers such as 15.

In some embodiments, the dimers of Formulae (III) and (IV) are preparedvia the method depicted in the following scheme:

where B¹ and B² are each independently a purine, a protected purine, apyrimidine or a protected pyrimidine, or an analog thereof; R¹⁵ ishydrogen or an amino protecting group; R¹⁷ is an amino protecting group;and R¹⁶ is a hydroxyl protecting group. In certain embodiments, R¹⁵ ishydrogen. In certain embodiments of monomer 16, R¹⁶ is a silyl. Incertain embodiments of monomer 16, R¹⁶ is TBDMS(tert-butyldimethylsilyl). In certain embodiments of monomer 17, R¹⁷ isa trityl (Trt). In certain embodiments of monomer 17, R¹⁷ is amonomethoxytrityl (MMT).

In certain embodiments of monomer 17, R¹⁷ is a dimethoxytrityl (DMT). Incertain embodiments of monomer 17, R¹⁷ is a pixyl. In certainembodiments of dimers 18-20, R¹⁷ is a trityl (Trt). In certainembodiments of dimers 18-20, R¹⁷ is a monomethoxytrityl (MMT). Incertain embodiments of dimers 18-20, R¹⁷ is a dimethoxytrityl (DMT). Incertain embodiments of dimers 18-20, R¹⁷ is a pixyl.

In some embodiments, the dimers of Formulae (III) and (IV) are preparedvia the method depicted in the following scheme, where the monomer 13 isprepared from 11 via monomer 12 and coupled with a nucleoside amidite toproduce dimers 14 which is converted to dimer 15:

where B¹ and B² are each independently a purine, a protected purine, apyrimidine or a protected pyrimidine, or an analog thereof; and R¹³ andR¹⁴ are each independently a protecting group. In certain embodiments ofmonomers 12 and 13, R¹³ is a trityl. In certain embodiments of monomers12 and 13, R¹³ is a pixyl. In certain embodiments of dimers 14 and 15,R¹⁴ is a trityl. In certain embodiments of dimers 14 and 15, R¹⁴ is adimethoxytrityl. In certain embodiments of dimers 14 and 15, R¹⁴ is amonomethoxytrityl. In certain embodiments of dimers 14 and 15, R¹⁴ is apixyl.

Monomers of interest that find use in preparation of the subjectdinucleotide dimers according to the methods described herein include,but are not limited to:

where B¹ is a purine, a protected purine, a pyrimidine or a protectedpyrimidine, or an analog thereof and R is hydrogen or an alkyl (e.g.,methyl) or a halogen (e.g., bromo). In certain cases, B¹ is selectedfrom A(Bz), G(iBu), T, A(DMF), C(Bz), or U.

Oligonucleotide Compositions

In addition to a target oligonucleotide, a variety of non-targetoligonucleotide synthesis products may be produced duringoligonucleotide synthesis. Minor products that may be present inoligonucleotide preparations include, but are not limited to, deletionproducts (e.g., products lacking one or more nucleoside residues),products that include one or more protecting groups, terminated products(e.g., products that include a capped oligonucleotide chain), productsthat lack one or more nucleobases, products that include partiallyoxidized phosphoramidite linkages and products that include partiallysulfurized linkages. As used herein, target oligonucleotide refers to anoligonucleotide sequence of interest, which is the target product of themethod of preparation. As used herein, the terms “non-target product”and “minor product” are used interchangeably and refer to anyoligonucleotide-containing product that is not the target product, andwhich may occur during and after the cycles of the targetoligonucleotide synthesis.

The subject methods provide for compositions that include an improvedpurity of target oligonucleotide. In some embodiments, the compositionincludes 50% or more by weight of the target oligonucleotide, such asabout 55% or more, about 60% or more, about 65% or more, about 70% ormore, about 75% or more, about 80% or more, about 85% or more, about 90%or more, or even about 95% or more by weight of the targetoligonucleotide. In certain embodiments, the composition includes 50% ormore by weight of the target oligonucleotide. In certain embodiments,the composition includes 55% or more by weight of the targetoligonucleotide. In certain embodiments, the composition includes 60% ormore by weight of the target oligonucleotide. In certain embodiments,the composition includes 65% or more by weight of the targetoligonucleotide. In certain embodiments, the composition includes 70% ormore by weight of the target oligonucleotide. In certain embodiments,the composition includes 75% or more by weight of the targetoligonucleotide. In certain embodiments, the composition includes 80% ormore by weight of the target oligonucleotide. In certain embodiments,the composition includes 85% or more by weight of the targetoligonucleotide. In certain embodiments, the composition includes 90% ormore by weight of the target oligonucleotide. In certain embodiments,the composition includes 95% or more by weight of the targetoligonucleotide.

In some embodiments, the subject methods provide for a couplingefficiency of 95% or more, such as 96% or more, 97% or more, 98% ormore, or even 98% or more.

In some embodiments, the subject methods provide for a mean couplingefficiency that is 0.5% or more, such as 0.75% or more, 1.0% or more,1.25% or more, 1.5% or more, 1.75% or more, 2.0% or more, 2.5% or more,or even 3.0% or more, than the mean coupling efficiency of a controlsynthesis performed using only monomer subunits. In certain embodiments,the subject methods provided for a 96% or greater coupling efficiency.In certain embodiments, the subject methods provides for a couplingefficiency that is 2% or greater than the coupling efficiency of acontrol synthesis performed using only monomer subunits.

After synthesis, the subject compositions may undergo one or morepurification steps (e.g., HPLC chromatography, affinity chromatography,ion exchange chromatography, gel filtration, etc.), e.g., to remove oneor more minor products from the target oligonucleotide. It is understoodthat, in the subject compositions, the reduced amounts of minor productsand/or increased amount of target oligonucleotide provided by thesubject methods of preparation may refer to such amounts and puritiesobtained immediately post synthesis and before any further purificationor separation steps (e.g., HPLC chromatography) have been performed. Assuch, in some cases, the subject compositions may be referred to assynthesis preparations, e.g., unpurified synthesis preparations. Byunpurified is meant that no chromatography purification steps have beenperformed on the composition. Chromatography purification refers to anyconvenient purification method that includes absorption of targetpolynucleotide to a chromatography support and subsequent elution of thetarget polynucleotide. In some cases, chromatography purification refersto reverse phase chromatography purification.

The subject methods provide for compositions including a reduced amountof one or more minor products. By reduced amount is meant that theamount by weight of the minor product in the composition relative to thetarget oligonucleotide is reduced relative to a control synthesis, e.g.,a synthesis where the oligonucleotide is prepared using only monomercouplings. In some embodiments, the reduced amount of minor product isabout 20% or less of the amount by weight of the target oligonucleotide,such as about 15% or less, about 10% or less, or about 5% or less of theamount by weight of the target oligonucleotide. In certain embodiments,the reduced amount of minor product is 20% or less of the amount byweight of the target oligonucleotide, such as 15% or less, 10% or less,9% or less, 8% or less, 7% or less, 6% or less, 5% or less, 4% or less,3% or less, 2% or less, or even 1% or less of the amount by weight ofthe target oligonucleotide. In certain embodiments, the minor product isa (N−x) product.

The subject methods of preparation may provide for compositions having areduced amount of one or more (N−x) products relative to a targetoligonucleotide of interest, where x is an integer from 1 to N−1 and Nis the number of nucleoside residues in the target oligonucleotide. Assuch, (N−1) product may refer to any and all oligonucleotide productsthat lack any one nucleotide residue in comparison to a targetoligonucleotide (e.g, a N product). As such, a (N−2) product refers toany and all oligonucleotide products that lack any two nucleotideresidues in comparison to a target oligonucleotide (e.g, a N product).In certain embodiments, the minor product is a (N−1) product. In certainembodiments, the minor product is a (N−2) product. In certainembodiments, the minor product is a (N−3) product. In certainembodiments, the minor product is a (N−4) product. In certainembodiments, the minor product is a (N−5) product. In certainembodiments, the minor product is a (N−6) product. In certainembodiments, the minor product is a (N−7) product.

In certain embodiments, any of the compositions described herein thathave a reduced amount of one or more (N−x) products relative to a targetoligonucleotide of interest are unpurified.

In some embodiments, the subject compositions include a low ratio of(N−1) product to target oligonucleotide product. In some cases, the lowratio is less than (2.0×N) parts to 100 parts by weight of (N−1) productrelative to target oligonucleotide, where N refers to the number ofnucleotide residues in the target oligonucleotide sequence. In certainembodiments, the ratio is less than (1.9×N) parts to 100 parts by weightof (N−1) product relative to target oligonucleotide, such as less than(1.8×N) parts to 100, less than (1.7×N) parts to 100, less than (1.6×N)parts to 100, less than (1.5×N) parts to 100, less than (1.4×N) parts to100, less than (1.3×N) parts to 100, less than (1.2×N) parts to 100,less than (1.1×N) parts to 100, less than (1.0×N) parts to 100, lessthan (0.9×N) parts to 100, less than (0.8×N) parts to 100, less than(0.7×N) parts to 100, less than (0.6×N) parts to 100, less than (0.5×N)parts to 100, less than (0.4×N) parts to 100, less than (0.3×N) parts to100, less than (0.2×N) parts to 100, or even less than (0.1×N) parts to100 parts by weight of (N−1) product relative to target oligonucleotide.In certain embodiments, the subject compositions include a low ratio ofless than (1.5×N) parts to 100 parts by weight of (N−1) product relativeto target oligonucleotide. In certain embodiments, the subjectcompositions include a low ratio of less than (1.2×N) parts to 100 partsby weight of (N−1) product relative to target oligonucleotide. Incertain embodiments, the subject compositions include a low ratio ofless than (1.0×N) parts to 100 parts by weight of (N−1) product relativeto target oligonucleotide. In certain embodiments, the subjectcompositions include a low ratio of less than (0.5×N) parts to 100 partsby weight of (N−1) product relative to target oligonucleotide.

In some embodiments, the subject compositions include a low ratio of(N−2) product to target oligonucleotide product. In some cases, the lowratio is less than (2.0×N) parts to 100 parts by weight of (N−2) productrelative to target oligonucleotide, where N refers to the number ofnucleotide residues in the target oligonucleotide sequence. In certainembodiments, the ratio is less than (1.9×N) parts to 100 parts by weightof (N−2) product relative to target oligonucleotide, such as less than(1.8×N) parts to 100, less than (1.7×N) parts to 100, less than (1.6×N)parts to 100, less than (1.5×N) parts to 100, less than (1.4×N) parts to100, less than (1.3×N) parts to 100, less than (1.2×N) parts to 100,less than (1.1×N) parts to 100, less than (1.0×N) parts to 100, lessthan (0.9×N) parts to 100, less than (0.8×N) parts to 100, less than(0.7×N) parts to 100, less than (0.6×N) parts to 100, less than (0.5×N)parts to 100, less than (0.4×N) parts to 100, less than (0.3×N) parts to100, less than (0.2×N) parts to 100, or even less than (0.1×N) parts to100 parts by weight of (N−2) product relative to target oligonucleotide.In certain embodiments, the subject compositions include a low ratio ofless than (1.5×N) parts to 100 parts by weight of (N−2) product relativeto target oligonucleotide. In certain embodiments, the subjectcompositions include a low ratio of less than (1.2×N) parts to 100 partsby weight of (N−2) product relative to target oligonucleotide. Incertain embodiments, the subject compositions include a low ratio ofless than (1.0×N) parts to 100 parts by weight of (N−1) product relativeto target oligonucleotide. In certain embodiments, the subjectcompositions include a low ratio of less than (0.5×N) parts to 100 partsby weight of (N−2) product relative to target oligonucleotide.

In some embodiments, the subject compositions include (N−1) product inan amount of 20% or less of the total non-target oligonucleotides in thecomposition, such as 15% or less, 10% or less or even 5% or less of thetotal non-target oligonucleotides.

Any of a wide variety of oligonucleotide compositions can be preparedusing the methods described herein. A variety of classes and types ofoligonucleotides are of interest for preparation using the subjectmethods (e.g., as described herein). Oligonucleotides suitable forpreparation according to the subject methods include, but are notlimited to, anti-sense oligonucleotides, RNA oligonucelotides, siRNAoligonucleotides, RNAi oligonucleotides, DNA aptamers, micro RNA, andthe like.

Oligonucleotides complementary to RNA component of Telomerase

Aspects of the disclosure include compounds and compositions includingoligonucleotides complementary to the RNA component of human telomerase,and methods for making the same. The compounds may inhibit telomeraseactivity in cells with a high potency and have cellular uptakecharacteristics.

As summarized above, the subject methods provide for reduced amounts ofnon-target oligonucleotide products of the synthesis. In certain cases,the subject methods provide for increase amounts of targetoligonucleotide product of the synthesis. In some embodiments, thesubject methods provide for the preparation of compositions that have areduced amount of one or more (N−x) products relative to a targetoligonucleotide of interest. Table 1 sets forth amounts of interest ofsome non-target oligonucleotide products.

In certain embodiments, any of the compositions described herein thathave a reduced amount of one or more (N−x) products relative to a targetoligonucleotide of interest are unpurified.

TABLE 1 Levels of oligonucleotide products in compositions of interest.The subject compositions may include one or more of the followingcomponents at one of the levels indicated in Table 1. Threshold AmountsRange relative to Range relative to % of composition relative to targettarget (by weight) target (by weight) Product (by weight) (by weight)Oligos imetelstat target 50% or more, N/A N/A N/A 55% or more, 60% ormore, 65% or more, 70% or more, 75% or more, 80% or more, 85% or more,90% or more, 95% or more (N-1) products less than 11% less than (1.9 ×N) from about (0.1 × from about 1 to (including less than 10% parts to100, less than N) to about (0.5 × about 20 parts in derivatives thereofless than 9% (1.8 × N) parts to 100, N) parts in 100, 100, from about 1such as Phenylacetyl less than 8% less than (1.7 × N) from about (0.1 ×to about 10 parts in and iBu derivatives) less than 7% parts to 100,less than N) to about (0.4 × 100, from about 1 (e.g., post peak 1 lessthan 6% (1.6 × N) parts to 100, N) parts in 100, to about 8 parts in(N-1) product) less than 5% less than (1.5 × N) from about (0.2 × 100,from about 1 less than 4% parts to 100, less than N) to about (0.3 × toabout 6 parts in less than 3% (1.4 × N) parts to 100, N) parts in 100,100, from about 1 less than 2% less than (1.3 × N) about (0.1 × N) toabout 5 parts in less than 1% parts to 100, less than parts in 100,about 100, from about 2 less than 0.5% (1.2 × N) parts to 100, (0.2 × N)parts in to about 4 parts in less than (1.1 × N) 100, about (0.3 × 100,parts to 100, less than N) parts in 100, about 1parts in (0.9 × N) partsto 100, about (0.4 × N) 100, about 2 parts less than (0.8 × N) parts in100, about in 100, about 3 parts to 100, less than (0.5 × N) parts inparts in 100, about (0.7 × N) parts to 100, 100, 4 parts in 100, lessthan (0.6 × N) about 5 parts in 100 parts to 100, less than less than 1part in (0.5 × N) parts to 100, 4, less than 1 part less than (0.4 × N)in 5, less than 1 parts to 100, less than part in 6, less than (0.3 × N)parts to 100, 1 part in 7, less less than (0.2 × N) than 1 part in 8,parts to 100, less than less than 1 part in (0.1 × N) parts to 100 9,less than 1 part in 10, less than 1 part in 20, less than 1 part in 25,less than 1 part in 100 (N-2) and (N-3) 4% or more at least (1.0 × N)parts from about (1.0 × from about 5 to products individually 6% or moreto 100, at least (1.5 × N) to about (5.0 × about 50 parts in or combined(including 8% or more N) parts to 100, at N) parts in 100, 100, fromabout 10 derivatives thereof 10% or more least (2.0 × N) parts to fromabout (2.0 × to about 50 parts in such as Phenylacetyl 12% or more 100,at least (2.5 × N) N) to about (5.0 × 100, from about 20 and iBuderivatives) 14% or more parts to 100, at least N) parts in 100, toabout 50 parts in (e.g., Post Peaks 16% or more (3.0 × N) parts to 100,from about (2.5 × 100, from about 30 2 + 3 + 4, or Post 18% or more atleast (3.3 × N) parts N) to about (4.0 × to about 50 parts in Peaks 3 +4, or post 20% or more to 100 N) parts in 100, 100, from about 5 Peak 2,3 or 4) 25% or more less than (3.3 × N) from about (3.0 × to about 40parts in less than 25% parts to 100, less than N) to about (4.0 × 100,from about 5 less than 20% (3.0 × N) parts to 100, N) parts in 100, toabout 30 parts in less than 18% less than (2.5 × N) from about (3.0 ×100, from about 5 less than 16% parts to 100, less than N) to about (3.5× to about 20 parts in less than 14% (2.0 × N) parts to 100, N) parts in100 100, from about 10 less than 12% less than (1.5 × N) about (1.0 × N)to about 20 parts in less than 10% parts to 100, less than parts in 100,about 100 (1.0 × N) parts to 100 (1.5 × N) parts in about 10 parts in100, about (2.0 × 100, about 15 parts N) parts in 100, in 100, about 20about (2.5 × N) parts in 100, about parts in 100, about 25 parts in 100,(3.0 × N) parts in about 30 parts in 100, about (3.3 × 100, about 35parts N) parts in 100, in 100, about 40 about (3.5 × N) parts in 100,about parts in 100 45 parts in 100, about 50 parts in 100 at least 5parts in 100, at least 10 parts in 100, at least 12 parts in 100, atleast 14 parts in 100, at least 15 parts in 100, at least 20 parts in100, at least 30 parts in 100, at least 40 parts in 100 Total non-target45% or less, less than (8.5 × N) from about (0.4 × from about 5 tooligonucleotides 40% or less, parts to 100, less than N) to about (5.0 ×about 50 parts in 35% or less, (8.0 × N) parts to 100, N) parts in 100,100, from about 10 30% or less, less than (7.5 × N) from about (0.8 × toabout 50 parts in 25% or less, parts to 100, less than N) to about (4.0× 100, from about 20 20% or less (7.0 × N) parts to 100, N) parts in100, to about 50 parts in less than (6.5 × N) from about (1.6 × 100,from about 20 parts to 100, less than N) to about (4.0 × to about 40parts in (6.0 × N) parts to 100, N) parts in 100, 100, from about 20less than (5.5 × N) from about (1.6 × to about 30 parts in parts to 100,less than N) to about (2.5 × 100, (5.0 × N) parts to 100, N) parts in100 about 25 parts in 100 less than (4.5 × N) about (1.9 × N) at least10 parts in parts to 100, less than parts to 100 100, at least 15 (4.0 ×N) parts to 100, at least (1.0 × N) parts in 100, at less than (3.5 × N)parts per 100, at least 20 parts in parts to 100, less than least (1.5 ×N) 100, at least 25 (3.0 × N) parts to 100, parts per 100, at parts in100, less than (2.5 × N) least (2.0 × N) less than 40 parts parts to100, less than parts per 100 in 100, less than 30 (2.0 × N) parts to100, parts in 100, less less than (1.5 × N) than 25 parts in parts to100, less than 100, less than 20 (1.0 × N) parts to 100 parts in 100,less than 15 parts in 100

In certain embodiments, the composition has less than (2.0×N) parts to100 parts by weight of (N−1) product relative to a compound, wherein thecompound includes a polynucleotide having a sequence of N nucleosidesubunits complementary to the RNA component of human telomerase, whereinat least two of the nucleoside subunits are joined by a N3′→P5′thiophosphoramidate inter-subunit linkage. In certain embodiments, theratio is less than (1.9×N) parts to 100 parts by weight of (N−1) productrelative to N product, such as less than (1.8×N) parts to 100, less than(1.7×N) parts to 100, less than (1.6×N) parts to 100, less than (1.5×N)parts to 100, less than (1.4×N) parts to 100, less than (1.3×N) parts to100, less than (1.2×N) parts to 100, less than (1.1×N) parts to 100,less than (1.0×N) parts to 100, less than (0.9×N) parts to 100, lessthan (0.8×N) parts to 100, less than (0.7×N) parts to 100, less than(0.6×N) parts to 100, less than (0.5×N) parts to 100, less than (0.4×N)parts to 100, less than (0.3×N) parts to 100, less than (0.2×N) parts to100, or even less than (0.1×N) parts to 100 parts by weight of (N−1)product relative to N product.

In some embodiments, the composition has less than 1 part in 4 by weightof a (N−1) product relative to a compound (such as, less than 1 part in5, less than 1 part in 6, less than 1 part in 7, less than 1 part in 8,less than 1 part in 9, less than 1 part in 10, less than 1 part in 15,less than 1 part in 20, less than 1 part in 25, less than 1 part in 50,less than 1 part in 100 by weight of a (N−1) product relative to acompound), wherein the compound comprises a polynucleotide having asequence of 10 or more nucleoside subunits complementary to the RNAcomponent of human telomerase, wherein at least two of the nucleosidesubunits are joined by a N3′→P5′ thiophosphoramidate oroxophosphoramidate inter-subunit linkage. In certain embodiments, thepolynucleotide has a sequence of 10 or more nucleoside subunitscomplementary to the RNA component of human telomerase, such as 10, 11,12, 13, 14, 15, 16, 17, 18, 19, 20 or more nucleoside subunits.

In certain instances, the polynucleotide includes a sequence of 13 ormore nucleoside subunits complementary to the RNA component of humantelomerase, such as 15 or more, 20 or more, 30 or more, 50 or morenucleoside subunits complementary to the RNA component of humantelomerase.

In certain embodiments, the polynucleotide includes a sequence of 7 ormore nucleoside subunits complementary to the RNA component of humantelomerase, such as 7, 8, 9, 10, 11, 12, 13, 14, 15, 16 or 17 nucleosidesubunits complementary to the RNA component of human telomerase. Incertain embodiments, the polynucleotide includes a sequence ofnucleoside subunits complementary to the RNA component of humantelomerase of between 11 and 18, such as between 11 and 16 contiguousnucleoside subunits complementary to the RNA component of humantelomerase.

In some embodiments, the polynucleotide includes between 3 and 50contiguous nucleoside subunits complementary to the RNA component ofhuman telomerase, such as between 5 and 40, between 10 and 40, between10 and 30, between 10 and 25, between 10 and 20, or between 12 and 15nucleoside subunits. In certain embodiments, the oligonucleotideincludes a sequence of 10 or more contiguous nucleoside subunitscomplementary to the RNA component of human telomerase. In certainembodiments, the composition has less than 1 part in 10 by weight of a(N−1) product relative to the compound. In certain embodiments, thecomposition has less than 1 part in 20 by weight of a (N−1) productrelative to the compound. In certain embodiments, the composition hasless than 1 part in 25 by weight of a (N−1) product relative to thecompound. In certain embodiments, the composition has less than 1 partin 30 by weight of a (N−1) product relative to the compound. In certainembodiments, the composition has less than 1 part in 50 by weight of a(N−1) product relative to the compound.

In some embodiments, the composition has less that 1 part in 4 by weightof any (N−x) product relative to the compound, such as less than 1 partin 5, less than 1 part in 6, less than 1 part in 7, less than 1 part in8, less than 1 part in 9, less than 1 part in 10, less than 1 part in20, less than 1 part in 25, less than 1 part in 30, or even less than 1part in 50 by weight, of any (N−x) product relative to the compound.

In some embodiments, the composition has less that 40 part in 100 bytotal weight of (N−x) polynucleotide-containing products relative to thecompound, such as less than 35 parts in 100, less than 30 parts in 100,less than 25 parts in 100, less than 20 parts in 100, or even less than15 parts in 100 by weight, of (N−x) polynucleotide-containing productsrelative to the compound.

In some embodiments, the composition has at least 5 parts in 100 byweight of (N−2) and (N−3) products relative to the compound, such as, atleast 10 parts in 100 by weight, at least 12 parts in 100 by weight, atleast 14 parts in 100 by weight, at least 15 parts in 100 by weight, atleast 20 parts in 100 by weight, at least 30 parts in 100 by weight, orat least 40 parts in 100 by weight of (N−2) and (N−3) products relativeto the compound.

In some embodiments, the composition has the following profile of (N−x)polynucleotide-containing products:

less that 1 part in 4 by weight of a (N−1) product relative to the Nproduct; and

at least 10 parts in 100 by weight of (N−2) and (N−3) products relativeto the N product.

In certain embodiments, the oligonucleotide N product comprises a3′-terminal nucleoside subunit that is absent in the (N−1) product.

The oligonucleotide compound may be described by the formula:

O-(x′-L′)_(n)

where O represents the oligonucleotide including a sequence ofnucleoside subunits complementary to the RNA component of humantelomerase, x′ is an optional linker group, L′ represents the lipidmoiety and n is an integer from 1-5.

Design of the compounds therefore requires the selection of twoentities, O and L′, and the determination of the structural linkage(s)between these entities, which may involve the optional linker group x′.

In some embodiments, the oligonucleotide compound may be described bythe formula:

O-(x′-L′)_(n)

where O represents the oligonucleotide including a sequence ofnucleoside subunits complementary to the RNA component of humantelomerase, x′ is an optional linker group, L′ represents the lipidmoiety and n is 1, such as an oligonucleotide of Formula (I), or a saltthereof, wherein in Formula (I), Z is the lipid moiety, L is theoptional linker and the B groups correspond to the sequence ofnucleoside subunits complementary to the RNA component of humantelomerase.

The oligonucleotide component O may be regarded as the “effector”component of the compound in that it is this component that effectsinhibition of the telomerase enzyme by binding to the RNA component oftelomerase. Thus, the sequence of O is selected such that it includes aregion that is complementary to the sequence of the telomerase RNA,which is shown in SEQ ID NO:1 The region that is complementary to thetelomerase RNA component may in theory be targeted to any portion of thetelomerase RNA, but particular regions of the telomerase RNA arepreferred target for inhibitory oligonucleotides. One preferred targetregion is the region spanning nucleotides 30-67 of SEQ ID NO:1, whichincludes the “template region,” an 11 nucleotide region of sequence5′-CUAACCCUAAC-3′ (SEQ ID NO: 2) that spans nucleotide 46-56 of SEQ IDNO: 1. The template region functions to specify the sequence of thetelomeric repeats that telomerase adds to the chromosome ends and isessential to the activity of the telomerase enzyme (see Chen at al.,Cell 100:503-514, 2000; Kim et al., Proc. Natl. Acad. Sci., USA98(14):7982-7987, 2001). Compounds of the invention that contain anoligonucleotide moiety comprising a sequence complementary to all orpart of the template region are thus particularly preferred. Anotherpreferred target region is the region spanning nucleotides 137-179 ofhTR (see Pruzan et al, Nucl. Acids Research, 30:559-588, 2002). Withinthis region, the sequence spanning 141-153 is a preferred target. PCTpublication WO 98/28442 describes the use of oligonucleotides of atleast 7 nucleotides in length to inhibit telomerase, where theoligonucleotides are designed to be complementary to accessible portionsof the hTR sequence outside of the template region, includingnucleotides 137-196, 290-319, and 350-380 of hTR.

The region of O that is targeted to the hTR sequence is preferablyexactly complementary to the corresponding hTR sequence. Whilemismatches may be tolerated in certain instances, they are expected todecrease the specificity and activity of the resultant oligonucleotideconjugate. In particular embodiments, the base sequence of theoligonucleotide O is thus selected to include a sequence of at least 5nucleotides exactly complementary to the telomerase RNA, and enhancedtelomerase inhibition may be obtained if increasing lengths ofcomplementary sequence are employed, such as at least 8, at least 10, atleast 12, at least 13 or at least 15 nucleotides exactly complementaryto the telomerase RNA. In other embodiments, the sequence of theoligonucleotide includes a sequence of from at least 5 to 20, from atleast 8 to 20, from at least 10 to 20 or from at least 10 to 15nucleotides exactly complementary to the telomerase RNA sequence.Optimal telomerase inhibitory activity may be obtained when the fulllength of the oligonucleotide O is selected to be complementary to thetelomerase RNA. However, it is not necessary that the full length of theoligonucleotide component be exactly complementary to the targetsequence, and the oligonucleotide sequence may include regions that arenot complementary to the target sequence. Such regions may be added, forexample, to confer other properties on the compound, such as sequencesthat facilitate purification. If the oligonucleotide component O is toinclude regions that are not complementary to the target sequence, suchregions may be positioned at one or both of the 5′ or 3′ termini. Ininstances where the region of exact complementarity is targeted to thetemplate region, effective telomerase inhibition may be achieved with ashort (5-8 nucleotide) region of exact complementarity to which atelomerase-like (G-rich) sequence is joined at the 5′ end.

Exemplary sequences that are complementary to the human telomerase RNAand which may be included as part of the oligonucleotide component 0, orwhich may be used as the entire oligonucleotide component O include thefollowing:

hTR complementary sequences (regions of Oligonucleotide sequence SEQ IDNO:1 of U.S. Publication 2012329858)

(SEQ ID NO: 1) GGGUUGCGGA GGGUGGGCCU GGGAGGGGUG GUGGCCAUUUUUUGUCUAAC CCUAACUGAG AAGGGCGUAG GCGCCGUGCUUUUGCUCCCC GCGCGCUGUU UUUCUCGCUG ACUUUCAGCGGGCGGAAAAG CCUCGGCCUG CCGCCUUCCA CCGUUCAUUCUAGAGCAAAC AAAAAAUGUC AGCUGCUGGC CCGUUCGCCCCUCCCGGGGA CCUGCGGCGG GUCGCCUGCC CAGCCCCCGAACCCCGCCUG GAGGCCGCGG UCGGCCCGGG GCUUCUCCGGAGGCACCCAC UGCCACCGCG AAGAGUUGGG CUCUGUCAGCCGCGGGUCUC UCGGGGGCGA GGGCGAGGUU CAGGCCUUUCAGGCCGCAGG AAGAGGAACG GAGCGAGUCC CCGCGCGCGGCGCGAUUCCC UGAGCUGUGG GACGUGCACC CAGGACUCGG CUCACACAUG C (SEQ ID NO: 6)GCTCTAGAATGAACGGTGGAAGGCGGCAGG 137-166 (SEQ ID NO: 7)GTGGAAGGCGGCAGG 137-151 (SEQ ID NO: 8) GGAAGGCGGCAGG 137-149(SEQ ID NO: 9) GTGGAAGGCGGCA 139-151 (SEQ ID NO: 10) GTGGAAGGCGG 141-151(SEQ ID NO: 11) CGGTGGAAGGCGG 141-153 (SEQ ID NO: 12)ACGGTGGAAGGCG 142-154 (SEQ ID NO: 13) AACGGTGGAAGGCGGC 143-155(SEQ ID NO: 14) ATGAACGGTGGAAGGCGG 144-158 (SEQ ID NO: 15)ACATTTTTTGTTTGCTCTAG 160-179 (SEQ ID NO: 3) TAGGGTTAGACAA 42-54(SEQ ID NO: 4) GTTAGGGTTAG 46-56 (SEQ ID NO: 16) GTTAGGGTTAGAC 44-56(SEQ ID NO: 17) GTTAGGGTTAGACAA 42-56 GGGTTAGAC 44-52 CAGTTAGGG 50-58(SEQ ID NO: 18) CCCTTCTCAGTT 54-65 (SEQ ID NO: 19) CGCCCTTCTCAG 56-67

In some embodiments, the polynucleotide comprises a sequence selectedfrom the group consisting of:

(SEQ ID NO: 4) GTTAGGGTTAG; (SEQ ID NO: 3) TAGGGTTAGACAA; and(SEQ ID NO: 5) CAGTTAGGGTTAG.

The choice of the type of inter-nucleoside linkages used in thesynthesis of the O component may be made from any of the availableoligonucleotide chemistries, including but not limited to,phosphodiester, phosphotriester, methylphosphonate, P3′→N5′phosphoramidate, N3′→P5′ phosphoramidate, N3′→P5′ thiophosphoramidate,and phosphorothioate linkages.

In some embodiments, the oligonucleotide component 0 has at least oneN3′→P5′ phosphoramidate (e.g., N3′→P5′ thiophosphoramidate) linkage. Incertain embodiments, the nucleoside subunits complementary to the RNAcomponent of human telomerase are all joined by N3′→P5′ phosphoramidateinter-subunit linkages. In certain cases, the N3′→P5′ phosphoramidateinter-subunit linkages are N3′→P5′ thiophosphoramidate inter-subunitlinkages. In certain cases, the N3′→P5′ phosphoramidate inter-subunitlinkages are N3′→P5′ oxo-phosphoramidate inter-subunit linkages.

In certain cases, the N3′→P5′ thiophosphoramidate inter-subunit linkagehas the following structure:

3′-NH—P(S)(OR)—O-5′

where R is selected from the group consisting of hydrogen, an alkyl, asubstituted alkyl, an aryl, a substituted aryl and a phosphateprotecting group. It is understood that some of the oligonucleotidecomponents 0 including an inter-subunit linkage described by the formulaabove where R is selected from the group consisting of hydrogen, analkyl, a substituted alkyl, an aryl, a substituted aryl and a phosphateprotecting group, may also exist in a salt form. Such forms in so far asthey may exist, are intended to be included within the scope of thepresent disclosure.

In some instances, the N3′→P5′ thiophosphoramidate inter-subunit linkageis described by the following structure:

3′-NH—P(S)(OR)—O-5′

where R is hydrogen. It is understood that for any of theoligonucleotide components O described herein that include such aninter-subunit linkage, such oligonucleotide components O may alsoinclude any convenient salt forms of the linkage. As such, theinter-subunit linkage may be in a salt form that includes any convenientcounterion.

The compounds of the invention are more effective in producingtelomerase inhibition in cells than corresponding oligonucleotides thatare not conjugated to lipid components. The lipid component L′ isbelieved to function to enhance cellular uptake of the compound,particularly in facilitating passage through the cellular membrane.While the mechanism by which this occurs has not been fully elucidated,one possibility is that the lipid component may facilitate binding ofthe compound to the cell membrane as either a single molecule, or anaggregate (micellar) form, with subsequent internalization. However,understanding of the precise mechanism is not required for the inventionto be utilized.

The lipid component may be any lipid or lipid derivative that providesenhanced cellular uptake compared to the unmodified oligonucleotide.Preferred lipids are hydrocarbons, fats (e.g., glycerides, fatty acidsand fatty acid derivatives, such as fatty amides) and sterols. Where thelipid component is a hydrocarbons, the L′ component may be a substitutedor unsubstituted cyclic hydrocarbon or an aliphatic straight chain orbranched hydrocarbon, which may be saturated or unsaturated. Preferredexamples are straight chain unbranched hydrocarbons that are fullysaturated or polyunsaturated. The length of the hydrocarbon chain mayvary from C2-C30, but optimal telomerase inhibition may be obtained withcarbon chains that are C8-C22. Preferred examples of saturatedhydrocarbons (alkanes) are listed below:

Systematic Name/Carbon Chain

Tetradecane C₁₄H₃₀

Pentadecane C₁₅H₃₂

Hexadecane C₁₆H₃₄

Heptadecane C₁₇H₃₆

Octadecane C₁₈H₃₈

Nonadecane C₁₉H₄₀

Eicosane C₂₀H₄₂

Mono- and poly-unsaturated forms (alkenes and polyenes, such asalkadienes and alkatrienes) of hydrocarbons may also be selected, withcompounds having one to three double bonds being preferred, althoughcompound having more double bonds may be employed. Alkynes (containingone or more triple bonds) and alkenynes (triple bond(s) and doublebond(s)) may also b utilized.

Substituted forms of hydrocarbons may be employed in the compounds ofthe invention, with substituent groups that are inert in vivo and invitro being preferred. A particularly preferred substituent is fluorine.Exemplary generic structures of polyfluorinated hydrocarbons include:CF₃(CF₂)_(n)—(CH₂)_(m)— where m is at least 1, preferably at least 2,and n=1-30, such as fluorotridecane: CF₃(CF₂)₉(CH₂)₃; andCH₃(CH₂)_(a)(CF₂)_(b)(CH₂)_(c)— where a, b and c are independently 1-30.

Other suitable lipid components include simple fatty acids and fattyacid derivatives, glycerides and more complex lipids such as sterols,for example cholesterol. Fatty acids and their derivatives may be fullysaturated or mono- or poly-unsaturated. The length of the carbon chainmay vary from C₂-C₃₀, but optimal telomerase inhibition may be obtainedwith carbon chains that are C₈-C₂₂. Preferred examples of saturatedfatty acids are listed below:

Systematic Name/Trivial Name/Carbon Chain

Tetradecanoic myristic 14:0

Hexadecanoic palmitic 16:0

Octadecanoic stearic 18:0

Eicosanoic arachidic 20:0

Mono- and poly-unsaturated forms of fatty acids may also be employed,with compounds having one to three double bonds being preferred,although compounds having more double bonds may also be employed.Examples of common mono- and poly-unsaturated fatty acids that may beemployed include:

Systematic Name/Trivial Name/Carbon Chain

Cis-9-hexadecanoic palmitoleic 16:1(n-7)

Cis-6-octadecanoic petroselinic 18:1 (n-12)

Cis-9-octadecanoic oleic 18:1 (n-9)

9,12-octadecadienoic linoleic 18:2 (n-6)

6,9,12-octadecatrienoic gamma-linoleic 18:3 (n-6)

9,12,15-octadecatrienoic alpha-linoleic 18:3 (n-3)

5,8,11,14-eicosatetraenoic arachidonic 20:4 (n-6)

Fatty acids with one or more triple bonds in the carbon chain, as wellas branched fatty acids may also be employed in the compounds of theinvention. Substituted forms of fatty acids may be employed in thecompounds of the invention. As with the hydrocarbon groups, substituentgroups that are inert in vivo and in vitro are preferred, with fluorinebeing a particularly preferred. Exemplary generic structures ofpolyfluorinated derivatives of fatty acids suitable for use in theinvention are: CF₃(CF₂)_(n)—(CH₂)_(m)CO— where m is at least 1,preferably at least 2, and n=1-30, and CH₃(CH₂)_(a)(CF₂)_(b)(CH₂)_(c)CO—where a, b and c are independently 1-30.

In some cases, between one and five L′ components (n=1-5) are covalentlylinked to the O component, optionally via a linker. More usually 1 ortwo L′ components are utilized (n=1 or 2). Where more than one L′component is linked to the O component, each L′ component isindependently selected.

It will be appreciated that compounds of the invention described ashaving a specified hydrocarbon as the L′ moiety and compounds describedas having a specified fatty acid (with the same number of carbon atomsas the specified hydrocarbon) are closely related and differ instructure only in the nature of the bond that joins the L′ moiety to theoligonucleotide, which in turn is a result of the synthesis procedureused to produce the compound. For example, and as described in moredetail below, when compounds are synthesized having the L′ moietyconjugated to the 3′-amino terminus of an oligonucleotide (havingphosphoramidate or thiophosphoramidate internucleoside linkages), theuse of the aldehyde form of a fatty acid (a fatty aldehyde) as thestarting material results in the formation of an amine linkage betweenthe lipid chain and the oligonucleotide, such that the lipid groupappears as a hydrocarbon. In contrast, use of the carboxylic acid, acidanhydride or acid chloride forms of the same fatty acid results in theformation of an amide linkage, such that the lipid group appears as afatly acid derivative, specifically in this instance a fatty amide (asnoted in the definitions section above, for the sake of simplicity, theterm “fatty acid” when describing the conjugated L′ group is usedbroadly herein to include fatty acid derivatives, including fattyamides). This is illustrated in the following schematics which depictthe 3′-amino terminus of a phosphoramidate oligonucleotide joined to aC14 lipid component. In schematic A, L′ is tetradecanoic acid (myristicacid), in which the connection between L′ and O groups is an amide. Inschematic B, L′ is tetradecane, and the connection between the L′ and Ogroups is an amine.

The linkage between the O and L′ components may be a direct linkage, ormay be via an optional linker moiety, e.g., x′ or optional linker L ofFormula (I). The linker group may serve to facilitate the chemicalsynthesis of the compounds. Whether or not a linker group is used tomediate the conjugation of the O and L′ components, there are multiplesites on the oligonucleotide component O to which the L′ component(s)may be conveniently conjugated. Suitable linkage points include the 5′and 3′ termini, one or more sugar rings, the internucleoside backboneand the nucleobases of the oligonucleotide. In some cases, the L′ moietyis attached to the 3′ or 5′ terminus of the oligonucleotide.

If the L′ component is to be attached to the 3′ terminus, the attachmentmay be directly to the 3′ substituent, which in the case of thepreferred phosphoramidate and thiophosphoramidate oligonucleotides isthe 3′-amino group, and in other instances, such as conventionalphosphodiester oligonucleotides, is a 3-hydroxy group. Alternatively,the L′ moiety may be linked via a 3′-linked phosphate group, in which ahexadecane hydrocarbon is linked to the 3′ phosphate of athiophosphoramidate oligonucleotide through an O-alkyl linker. If the L′moiety is to be linked to the 5′ terminus, it may be attached through a5′-linked phosphate group. Attachment to a base on the O moiety maythrough any suitable atom, for example to the N2 amino group ofguanosine. Where n>1 such that a plurality of lipid moieties is to beattached to the O component, the individually selected L′ components maybe attached at any suitable site(s). For example, one L′ group may beattached to each terminus, various L′ groups may be attached to thebases, or two or more L′ groups may be attached at one terminus.

The optional linker component x′ may be used to join the O and L′components of the compounds. It is understood that the optional linker(e.g., x′, or L of Formula (I)) may be attached to the polynucleotide(e.g., O) through a terminal phosphate group, e.g., a 3′-linked or a5′-linked phosphate group. If a linker is to be employed, it isincorporated into the synthesis procedures as described herein. Examplesof suitable linker groups include amino glycerol and O-alkylglycerol-type linkers which respectively can be depicted by the genericstructures:

wherein R′═H, OH, NH₂ or SH; Y═O, S or NR; R═H, an alkyl or asubstituted alkyl; and n and m are independently integers between 1-18.

Specific examples of suitable linkers are the aminoglycerol linker inwhich R′═OH, Y═O, and m and n are each 1:

the bis-aminoglycerol linker, in which R′═OH, Y═NH, and m and n are each1:

and the O-alkyl glycerol linker in which R═H:

Exemplary lipid-modified oligonucleotides that may be prepared accordingto the subject methods include those compounds described in FIG. 1(e.g., FIGS. 1A-1DD) of U.S. Application US20120329858 to Gryaznov et al“Modified oligonucleotides for telomerase inhibition”, the disclosure ofwhich is herein incorporated by reference in its entirety.

In certain embodiments, the composition includes a compound described bythe structure:

where “nps” represents a thiophosphoramidate linkage (e.g.,—NH—P(═O)(SH)—O—), connecting the 3′-carbon of one nucleoside to the5′-carbon of the adjacent nucleoside.

It is understood that all embodiments referring to a compound are alsoapplicable to the salt forms of said compound.

In certain embodiments, the composition includes a compound described bythe structure:

or a salt thereof;where “nps” represents a thiophosphoramidate linkage (e.g.,—NH—P(═O)(SH)—O— or a tautomer thereof, or a salt thereof), connectingthe 3′-carbon of one nucleoside to the 5′-carbon of the adjacentnucleoside. In certain embodiments, the composition includes apharmaceutically acceptable salt of the compound. In certain instances,the composition includes a sodium salt of the compound. In certainembodiments, the composition includes a divalent cation salt of thecompound, such as a magnesium salt of the compound. In certainembodiments, the composition includes a trivalent cation salt of thecompound, such as an aluminium salt of the compound.

In certain embodiments, the composition includes an oligonucleotidedescribed by the following structure, where each M^(x+) is independentlyhydrogen or any convenient counterion of a salt, each x is independently1, 2 or 3 and n is an integer from 5 to 13, such as 5, 6, 7, 8, 9, 10,11, 12 or 13, such as n is 13:

In certain instances, each x is 1. In certain instances, each x isindependently 1 or 2. In certain instances, each x is independently 1 or3. In certain instances, M^(x+) is hydrogen.

In certain embodiments, the composition includes an oligonucleotidedescribed by the following structure and may include any convenientcationic counterions of a salt:

In certain embodiments, the composition includes a compound described bythe structure:

Also provided are compound active pharmaceutical ingredient compositionsincluding an oligonucleotide-containing compound. As used herein, anactive pharmaceutical ingredient refers to a composition that isproduced using the subject methods of preparation, where the compositionmay optionally be subjected to one or more further purification stepspost synthesis. In general, an active pharmaceutical ingredient is acomposition suitable for formulation into a pharmaceutical composition.In some cases, the compound active pharmaceutical ingredient compositionis not purified post synthesis, such that the oligonucleotide-containingcomponents of the composition reflect those products produced duringoligonucleotide synthesis.

In some embodiments, the compound active pharmaceutical ingredient hasless than 9% by weight of a (N−1) product, wherein the compoundcomprises a polynucleotide having a sequence of 10 or more nucleosidesubunits complementary to the RNA component of human telomerase, whereinat least two of the nucleoside subunits are joined by a N3′→P5′thiophosphoramidate or oxophosphoramidate inter-subunit linkage (e.g.,as described herein).

In some embodiments, the compound active pharmaceutical ingredient hasless than 9% by weight of a (N−1) product, wherein the compound or apharmaceutically acceptable salt thereof comprises a polynucleotidehaving a sequence of 10 or more nucleoside subunits complementary to theRNA component of human telomerase, wherein at least two of thenucleoside subunits are joined by a N3′→P5′ thiophosphoramidate oroxophosphoramidate inter-subunit linkage (e.g., as described herein).

In some embodiments of the compound active pharmaceutical ingredient,the nucleoside subunits complementary to the RNA component of humantelomerase are all joined by N3′→P5′ thiophosphoramidate inter-subunitlinkages.

In some embodiments of the compound active pharmaceutical ingredient,the N3′→P5′ thiophosphoramidate inter-subunit linkage has the followingstructure:

3′-NH—P(S)(OR)—O-5′

where R is selected from the group consisting of hydrogen, an alkyl, asubstituted alkyl, an aryl, a substituted aryl and a phosphateprotecting group. When R is selected from the group consisting ofhydrogen, an alkyl, a substituted alkyl, an aryl, a substituted aryl anda phosphate protecting group, it is understood that some of theinter-subunit linkages described by the formula above may also exist ina salt form. Such forms in so far as they may exist, are intended to beincluded within the scope of the present disclosure.

In some embodiments of the compound active pharmaceutical ingredient,the N3′→P5′ thiophosphoramidate inter-subunit linkage has the followingstructure:

3′-NH—P(S)(OR)—O-5′

where R is hydrogen. It is understood that for any of the compoundactive pharmaceutical ingredients described herein that include such aninter-subunit linkage, such compound active pharmaceutical ingredientmay also include any convenient pharmaceutically acceptable salt formsof the linkage. As such, the inter-subunit linkage may be in apharmaceutically acceptable salt form that includes any convenientcounterion of the salt.

In some embodiments of the compound active pharmaceutical ingredient,the polynucleotide comprises between 10 and 50 contiguous nucleosidesubunits complementary to the RNA component of human telomerase (e.g.,as described herein).

In some embodiments of the compound active pharmaceutical ingredient,the polynucleotide comprises a sequence selected from the groupconsisting of:

(SEQ ID NO: 4) GTTAGGGTTAG; (SEQ ID NO: 3) TAGGGTTAGACAA; and(SEQ ID NO: 5) CAGTTAGGGTTAG.

In some embodiments of the compound active pharmaceutical ingredient,the polynucleotide includes a 3′amino or a 3′-hydroxyl terminal group.In certain embodiments of the compound active pharmaceutical ingredient,the polynucleotide includes a 3′amino terminal group. In certainembodiments of the compound active pharmaceutical ingredient, thepolynucleotide includes a 3′-hydroxyl terminal group.

In some embodiments of the compound active pharmaceutical ingredient,the compound has the structure:

wherein “nps” represents a thiophosphoramidate linkage —NH—P(═O)(SH)—O—,connecting the 3′-carbon of one nucleoside to the 5′-carbon of theadjacent nucleoside.

It is understood that all embodiments referring to a compound activepharmaceutical ingredient are also applicable to the salt forms of saidcompound active pharmaceutical ingredient.

In some embodiments of the compound active pharmaceutical ingredient,the compound has the structure:

or a pharmaceutically acceptable salt thereof;wherein “nps” represents a thiophosphoramidate linkage —NH—P(═O)(SH)—O—(or a tautomer thereof or a pharmaceutically acceptable salt thereof, asdescribed herein), connecting the 3′-carbon of one nucleoside to the5′-carbon of the adjacent nucleoside. In certain embodiments of thecompound active pharmaceutical ingredient, the composition includes asodium salt of the compound. In certain embodiments, the compositionincludes a divalent cation salt of the compound, such as a magnesiumsalt of the compound. In certain embodiments, the composition includes atrivalent cation salt of the compound, such as an aluminium salt of thecompound.

In certain embodiments of the compound active pharmaceutical ingredient,the compound is described by the following structure, where each M^(x+)is independently hydrogen or any convenient counterion of a salt, each xis independently 1, 2 or 3 and n is an integer from 5 to 13, such as 5,6, 7, 8, 9, 10, 11, 12 or 13, such as n is 13:

In certain instances, each x is 1. In certain instances, each x isindependently 1 or 2. In certain instances, each x is independently 1 or3. In certain instances, M^(x+) is hydrogen.

In certain embodiments of the compound active pharmaceutical ingredient,the compound is described by the following structure and may include anyconvenient cationic counterions of a salt:

In some embodiments of the compound active pharmaceutical ingredient,the compound is described by the structure:

In some embodiments, the compound active pharmaceutical ingredient hasless that 9% by weight of the (N−1) product, such as less than 8% byweight, less than 7% by weight, less than 6% by weight, less than 5% byweight, less than 4% by weight, less than 3% by weight, less than 2% byweight, or even less than 1% by weight of the (N−1) product. In certainembodiments, the compound active pharmaceutical ingredient has less that5% by weight of the (N−1) product. In certain embodiments, the compoundactive pharmaceutical ingredient has less that 2% by weight of the (N−1)product.

In some embodiments, the active pharmaceutical ingredient has less that9% of any (N−x) product, such as less than 8% by weight, less than 7% byweight, less than 6% by weight, less than 5% by weight, less than 4% byweight, less than 3% by weight, less than 2% by weight, or even lessthan 1% by weight of any (N−x) product.

In some embodiments, the compound active pharmaceutical ingredient hasless that 9% by weight in total of (N−x) polynucleotide-containingproducts, such as less than 8% by weight, less than 7% by weight, lessthan 6% by weight, less than 5% by weight, less than 4% by weight, lessthan 3% by weight, less than 2% by weight, or even less than 1% byweight in total of (N−x) polynucleotide-containing products.

In some embodiments, the compound active pharmaceutical ingredient hasthe following profile of (N−x) polynucleotide-containing products:

less that 1 part in 4 by weight of a (N−1) product relative to the Nproduct; and

at least 10 parts in 100 by weight of (N−2) and (N−3) products relativeto the N product.

Formulations

Also provided are pharmaceutical compositions that include anoligonucleotide composition (e.g., as described herein). Theoligonucleotide compositions (e.g., as described herein) can also beformulated as a pharmaceutical composition for inhibition oftranscription or translation in a cell in a disease condition related tooverexpression of the target gene.

In some embodiments, the pharmaceutical composition includes anoligonucleotide composition (e.g., as described herein) formulated in apharmaceutically acceptable excipient. In certain embodiments, theoligonucleotide composition is a compound active pharmaceuticalingredient having less than 9% by weight of a (N−1) product, wherein thecompound comprises a polynucleotide having a sequence of 10 or morenucleoside subunits complementary to the RNA component of humantelomerase, wherein at least two of the nucleoside subunits are joinedby a N3′→P5′ thiophosphoramidate inter-subunit linkage.

The present invention provides compounds that can specifically andpotently inhibit telomerase activity, and which may therefore be used toinhibit the proliferation of telomerase-positive cells, such as tumorcells. A very wide variety of cancer cells have been shown to betelomerase-positive, including cells from cancer of the skin, connectivetissue, adipose, breast, lung, stomach, pancreas, ovary, cervix, uterus,kidney, bladder, colon, prostate, central nervous system (CNS), retinaand hematologic tumors (such as myeloma, leukemia and lymphoma). Cancersof interest include, but are not limited to, myelofibrosis,thrombocythemia, myelodysplasic syndrome and myelogenous leukemia.

The subject compounds can be used to treat hematologic malignancies andmyeloproliferative disorders, including but not limited to, essentialthrombocythemia (ET), polycythemia vera (PV) chronic myelogenousleukemia (CML), myelofibrosis (MF), chronic neutrophilic leukemia,chronic eosinophilic leukemia, and acute myelogenous leukemia (AML). Thesubject compounds can be used to treat myelodysplastic syndromes, whichinclude such disease as refractory anemia, refractory anemia with excessblasts, refractory cytopenia with multilineage dysplasia, refractorycytopenia with unilineage dysplasia, and chronic myelomonocytic leukemia(CMML). The subject compounds can be used to treat hematologicaldiseases, such as those described in PCT patent application No.PCT/US13/070437 filed Nov. 15, 2013, the disclosure of which isincorporated herein by reference in its entirety.

Accordingly, the compounds provided herein are broadly useful intreating a wide range of malignancies. More importantly, the compoundsof the present invention can be effective in providing treatments thatdiscriminate between malignant and normal cells to a high degree,avoiding many of the deleterious side-effects present with most currentchemotherapeutic regimens which rely on agents that kill dividing cellsindiscriminately. Moreover, the compounds of the invention are morepotent than equivalent unconjugated oligonucleotides, which means thatthey can be administered at lower doses, providing enhanced safety andsignificant reductions in cost of treatment. One aspect of the inventiontherefore is a method of treating cancer in a patient, comprisingadministering to the patient a therapeutically effective dose of acompound of the present invention. Telomerase inhibitors, includingcompounds of the invention, may be employed in conjunction with othercancer treatment approaches, including surgical removal of primarytumors, chemotherapeutic agents and radiation treatment. Hence, theinvention relates to compounds and compositions provided herein for useas a medicament. The invention also relates to compounds andcompositions provided herein for use in treating or preventing any oneof the malignancies mentioned hereinbefore.

For therapeutic application, a compound of the invention is formulatedin a therapeutically effective amount with a pharmaceutically acceptablecarrier. One or more invention compounds (for example, having differentL′ or O components) may be included in any given formulation. Thepharmaceutical carrier may be solid or liquid. Liquid carriers can beused in the preparation of solutions, emulsions, suspensions andpressurized compositions. The compounds are dissolved or suspended in apharmaceutically acceptable liquid excipient. Suitable examples ofliquid carriers for parenteral administration of the oligonucleotidespreparations include water (which may contain additives, e.g., cellulosederivatives, preferably sodium carboxymethyl cellulose solution),phosphate buffered saline solution (PBS), alcohols (including monohydricalcohols and polyhydric alcohols, e.g., glycols) and their derivatives,and oils (e.g., fractionated coconut oil and arachis oil). The liquidcarrier can contain other suitable pharmaceutical additives including,but not limited to, the following: solubilizers, suspending agents,emulsifiers, buffers, thickening agents, colors, viscosity regulators,preservatives, stabilizers and osmolarity regulators.

For parenteral administration of the compounds, the carrier can also bean oily ester such as ethyl oleate and isopropyl myristate. Sterilecarriers are useful in sterile liquid form compositions for parenteraladministration.

Sterile liquid pharmaceutical compositions, solutions or suspensions canbe utilized by, for example, intraperitoneal injection, subcutaneousinjection, intravenously, or topically. The oligonucleotides can also beadministered intravascularly or via a vascular stent.

The liquid carrier for pressurized compositions can be a halogenatedhydrocarbon or other pharmaceutically acceptable propellant. Suchpressurized compositions may also be lipid encapsulated for delivery viainhalation. For administration by intranasal or intrabronchialinhalation or insufflation, the oligonucleotides may be formulated intoan aqueous or partially aqueous solution, which can then be utilized inthe form of an aerosol.

The compounds may be administered topically as a solution, cream, orlotion, by formulation with pharmaceutically acceptable vehiclescontaining the active compound.

The pharmaceutical compositions of this invention may be orallyadministered in any acceptable dosage including, but not limited to,formulations in capsules, tablets, powders or granules, and assuspensions or solutions in water or non-aqueous media. Pharmaceuticalcompositions and/or formulations comprising the oligonucleotides of thepresent invention may include carriers, lubricants, diluents,thickeners, flavoring agents, emulsifiers, dispersing aids or binders.In the case of tablets for oral use, carriers which are commonly usedinclude lactose and corn starch. Lubricating agents, such as magnesiumstearate, may also be added. For oral administration in a capsule form,useful diluents include lactose and dried corn starch. When aqueoussuspensions are required for oral use, the active ingredient is combinedwith emulsifying and suspending agents. If desired, certain sweetening,flavoring or coloring agents may also be added.

While the compounds of the invention have superior characteristics forcellular and tissue penetration, they may be formulated to provide evengreater benefit, for example in liposome carriers. The use of liposomesto facilitate cellular uptake is described, for example, in U.S. Pat.Nos. 4,897,355 and 4,394,448. Numerous publications describe theformulation and preparation of liposomes. The compounds can also beformulated by mixing with additional penetration enhancers, such asunconjugated forms of the lipid moieties described above, includingfatty acids and their derivatives. Examples include oleic acid, lauricacid, capric acid, myristic acid, palmitic acid, stearic acid, linoleicacid, linolenic acid, dicaprate, tricaprate, recinleate, monoolein(a.k.a. 1-monooleoyl-rac-glycerol), dilaurin, caprylic acid, arichidonicacid, glyceryl 1-monocaprate, 1-dodecylazacycloheptan-2-one,acylcarnitines, acylcholines, mono- and di-glycerides andphysiologically acceptable salts thereof (i.e., oleate, laurate,caprate, myristate, palmitate, stearate, linoleate, etc.).

Complex formulations comprising one or more penetration enhancing agentsmay be used. For example, bile salts may be used in combination withfatty acids to make complex formulations. Exemplary combinations includechenodeoxycholic acid (CDCA), generally used at concentrations of about0.5 to 2%, combined with sodium caprate or sodium laurate, generallyused at concentrations of about 0.5 to 5%.

Pharmaceutical compositions and/or formulations comprising theoligonucleotides of the present invention may also include chelatingagents, surfactants and non-surfactants. Chelating agents include, butare not limited to, disodium ethylenediaminetetraacetate (EDTA), citricacid, salicylates (e.g., sodium salicylate, 5-methoxysalicylate andhomovanilate), N-acyl derivatives of collagen, laureth-9 and N-aminoacyl derivatives of beta-diketones (enamines). Surfactants include, forexample, sodium lauryl sulfate, polyoxyethylene-9-lauryl ether andpolyoxyethylene-20-cetyl ether; and perfluorochemical emulsions, such asFC-43. Non-surfactants include, for example, unsaturated cyclic ureas,1-alkyl- and 1-alkenylazacyclo-alkanone derivatives, and non-steroidalanti-inflammatory agents such as diclofenac sodium, indomethacin andphenylbutazone.

Thus, in another aspect of the invention, there is provided a method offormulating a pharmaceutical composition, the method comprisingproviding a compound as described herein, and combining the compoundwith a pharmaceutically acceptable excipient. Preferably the compound isprovided at pharmaceutical purity, as defined below. The method mayfurther comprise adding to the compound, either before or after theaddition of the excipient, a penetration enhancing agent.

The pharmaceutical composition may comply with pharmaceutical puritystandards. In some cases, for use as an active ingredient in apharmaceutical preparation, a subject compound is purified away fromreactive or potentially immunogenic components present in the mixture inwhich they are prepared.

The pharmaceutical composition may be aliquoted and packaged in eithersingle dose or multi-dose units. The dosage requirements for treatmentwith the oligonucleotide compound vary with the particular compositionsemployed, the route of administration, the severity of the symptomspresented, the form of the compound and the particular subject beingtreated.

Pharmaceutical compositions of the invention can be administered to asubject in a formulation and in an amount effective to achieve aclinically desirable result. For the treatment of cancer, desirableresults include reduction in tumor mass (as determined by palpation orimaging; e.g., by radiography, radionucleotide scan, CAT scan, or MRI),reduction in the rate of tumor growth, reduction in the rate ofmetastasis formation (as determined e.g., by histochemical analysis ofbiopsy specimens), reduction in biochemical markers (including generalmarkers such as ESR, and tumor-specific markers such as serum PSA), andimprovement in quality of life (as determined by clinical assessment,e.g., Karnofsky score), increased time to progression, disease-freesurvival and overall survival.

The amount of compound per dose and the number of doses required toachieve such effects will vary depending on many factors including thedisease indication, characteristics of the patient being treated and themode of administration. In some instances, the formulation and route ofadministration will provide a local concentration at the disease site ofbetween 1 kM and 1 nM of the compound.

In general, the compounds are administered at a concentration thataffords effective results without causing any harmful or deleteriousside effects. Such a concentration can be achieved by administration ofeither a single unit dose, or by the administration of the dose dividedinto convenient subunits at suitable intervals throughout the day.

Utility

The methods and compositions of the invention, e.g., as described above,find use in a variety of applications. Applications of interest include,but are not limited to: therapeutic applications, diagnosticapplications, research applications, and screening applications, asreviewed in greater detail below.

The subject compounds find use in a variety of therapeutic applications.In some embodiments, the methods of producing an oligonucleotide areapplied to prepare oligonucleotides that provide for a therapeuticbenefit. The types of diseases which are treatable using thecompositions of the present invention are limitless. For example, thecompositions may be used for treatment of a number of genetic diseases.In some embodiments, the subject methods and compositions have antisenseapplications. In some embodiments, the subject methods and compositionshave antigene applications. In certain embodiments, the subject methodsand compositions have telomerase inhibition applications, such as thosedescribed in U.S. Pat. No. 6,835,826, and U.S. Publication 20120329858,the disclosures of which are herein incorporated by reference in theirentirety.

The subject compounds and methods find use in a variety of diagnosticapplications, including but not limited to, the development of clinicaldiagnostics, e.g., in vitro diagnostics or in vivo tumor imaging agents.Such applications are useful in diagnosing or confirming diagnosis of adisease condition, or susceptibility thereto. The methods are alsouseful for monitoring disease progression and/or response to treatmentin patients who have been previously diagnosed with the disease.

EXAMPLES

The following examples are put forth so as to provide those of ordinaryskill in the art with a complete disclosure and description of how tomake and use the present invention, and are not intended to limit thescope of what the inventors regard as their invention nor are theyintended to represent that the experiments below are all or the onlyexperiments performed. Efforts have been made to ensure accuracy withrespect to numbers used (e.g. amounts, temperature, etc.) but someexperimental errors and deviations should be accounted for. Unlessindicated otherwise, parts are parts by weight, molecular weight isweight average molecular weight, temperature is in degrees Celsius, andpressure is at or near atmospheric. By “average” is meant the arithmeticmean. Standard abbreviations may be used, e.g., bp, base pair(s); kb,kilobase(s); pl, picoliter(s); s or sec, second(s); min, minute(s); h orhr, hour(s); aa, amino acid(s); kb, kilobase(s); bp, base pair(s); nt,nucleotide(s); i.m., intramuscular(ly); i.p., intraperitoneal(ly); s.c.,subcutaneous(ly); and the like.

General Synthetic Procedures

Many general references providing commonly known chemical syntheticschemes and conditions useful for synthesizing the disclosed compoundsare available (see, e.g., Smith and March, March's Advanced OrganicChemistry: Reactions, Mechanisms, and Structure, Fifth Edition,Wiley-Interscience, 2001; or Vogel, A Textbook of Practical OrganicChemistry, Including Qualitative Organic Analysis, Fourth Edition, NewYork: Longman, 1978).

Compounds as described herein can be purified by any purificationprotocol known in the art, including chromatography, such as HPLC,preparative thin layer chromatography, flash column chromatography andion exchange chromatography. Any suitable stationary phase can be used,including normal and reversed phases as well as ionic resins. In certainembodiments, the disclosed compounds are purified via silica gel and/oralumina chromatography. See, e.g., Introduction to Modern LiquidChromatography, 2nd Edition, ed. L. R. Snyder and J. J. Kirkland, JohnWiley and Sons, 1979; and Thin Layer Chromatography, ed E. Stahl,Springer-Verlag, New York, 1969.

During any of the processes for preparation of the subject compounds, itmay be necessary and/or desirable to protect sensitive or reactivegroups on any of the molecules concerned. This may be achieved by meansof conventional protecting groups as described in standard works, suchas J. F. W. McOmie, “Protective Groups in Organic Chemistry”, PlenumPress, London and New York 1973, in T. W. Greene and P. G. M. Wuts,“Protective Groups in Organic Synthesis”, Third edition, Wiley, New York1999, in “The Peptides”; Volume 3 (editors: E. Gross and J. Meienhofer),Academic Press, London and New York 1981, in “Methoden der organischenChemie”, Houben-Weyl, 4^(Y) edition, Vol. 15/1, Georg Thieme Verlag,Stuttgart 1974, in H.-D. Jakubke and H. Jescheit, “Aminosauren, Peptide,Proteine”, Verlag Chemie, Weinheim, Deerfield Beach, and Basel 1982,and/or in Jochen Lehmann, “Chemie der Kohlenhydrate: Monosaccharide andDerivate”, Georg Thieme Verlag, Stuttgart 1974. The protecting groupsmay be removed at a convenient subsequent stage using methods known fromthe art.

The subject compounds can be synthesized via a variety of differentsynthetic routes using commercially available starting materials and/orstarting materials prepared by conventional synthetic methods. A varietyof examples of synthetic routes that can be used to synthesize thecompounds disclosed herein are described in the schemes below.

Example 1 Synthesis of Imetelstat Sodium Using Dimeric Phosphoramidites

Imetelstat sodium is synthesized using a solid support (Controlled poreglass or polymeric solid support) and monomer phosphoramidites such asA^(Bz) or A^(dmf), C, G^(iBu) and T amidites in the following sequence:

(SEQ ID NO: 3) 5′R-TAGGGTTAGACAA-NH₂-3′ where R = Lipid linker group

TABLE 2 Structure of the Amidites and Solid Support Abbreviated NameDescription Structure Amidite A^(dmf) 3′-Tritylamino-N₆-dimethylformamidino- 2′,3′-dideoxyadenosine- 5′-(2-cyanoethyl)-N,N-diisopropyl Phosphoramidite

Amidite A^(dmf) ^((MMT)) 3′- Monomethoxytritylamino-N₆-dimethylformamidino- 2′,3′-dideoxyadenosine- 5′-(2-cyanoethyl)-N,N-diisopropyl Phosphoramidite

Amidite A^(dmf) (pixyl) 3′-(Dimethyl-substituted Pixyl)amino-N₆-dimethylformamidino- 2′,3′-dideoxyadenosine- 5′-(2-cyanoethyl)-N,N-diisopropyl Phosphoramidite

Amidite A^(dmf) (DMT) 3′-Dimethoxytritylamino- N₆-dimethylformamidino-2′,3′-dideoxyadenosine- 5′-(2-cyanoethyl)-N,N- diisopropylPhosphoramidite

Amidite A^(Bz) 3′-Tritylamino-N₆- benzoyl-2∝,3′- dideoxyadenosine-5′-(2-cyanoethyl)-N,N- diisopropyl Phosphoramidite

Amidite C(Bz) 3′-Tritylamino-N- benzoyl-2′,3′- dideoxycytidine 5′-(2-cyanoethyl)- N,N- diisopropylphosphoramidite

Amidite G(iBu) 3′-Tritylamino-N2- isobutyry1-2,3-dideoxyguanosine-5′-(2- cyanoethyl)-N,N- diisopropyl Phosphoramidite

Amidite T 3′-Tritylamino-3′- deoxythymidine 5′-(2- cyanoethyl)-N,N-diisopropylphosphoramidite

Palmitoyl- aminoglycerol - solid support Or 3-palmitoylamido-1-O-(4,4′-dimethoxytrity1)-2- O-succinyl propanediol Controlled Pore GlassSupport

NittoPhaseHL Palmitoyl 400 Polymeric Solid Support 3-palmitoylamido-1-O-(4,4′-dimethoxytrity1)-2- O-succinyl propanediol Polymeric Solid Support

The imetelstat backbone is NPS which is similar to startingphosphoramidites and therefore the coupling efficiency is approximately92%. Utilization of dimer phosphoramidites allows fewer coupling stepswhich can lead to higher yield and purity at the intermediate stageafter synthesis. The following dimer phosphoramidites were prepared asshown below using a method as described in synthetic scheme 1:

TA, AA, GA, GG and GT.

The synthesis of the dimer phosphoramidites required three monomeramidates (4a to 4c, scheme 1) and three 5′-TBDMS-3′ amino nucleosideintermediates (3a to 3c, scheme 1) for A, G and T nucleosides. TBDMS istert-butyldimethylsilyl. The intermediates (3a to 3c, scheme 1) wereprepared from two kinds of starting materials,5′-OH-3′-NH-Tr-2′-deoxy-N-benzoyl adenosine (1a),5′-OH-3′-NH-Tr-2′-deoxy-N-isobutyryl guanosine (1b), and5′-OH-3′-amino-thymidine (2). Tr or Trt refer to trityl.

The 5′-hydroxyl group of 1a and 1b were protected with TBDMS groupsusing t-butyldimethylsilyl chloride and imidazole in DMF(N,N-dimethylformamide), and then the trityl groups at the 3′-aminopositions were deprotected by the treatment with acetic acid in water.The resulting intermediates, 3a to 3c were coupled with thecorresponding amidates, 4a to 4c, using benzylmercaptotetrazole (BMT) asan activator in dimethylformamide and the subsequent sulfurization (PIII to P V) was performed using xanthane hydride and pyridine (scheme1). In general, the sulfurization reaction was completed easily. Theoutcomes of the coupling reactions varied depending on moisture,reaction time, and equivalency of amidates. Anhydrous conditions usingnitrogen or argon gas and a quick coupling reaction was desirable sincea longer reaction time lead to more side products such as P (V)oxidation products. The P (III) intermediates of the dimer havedifferent stabilities. The TA intermediate was stable enough to monitorthe reaction completion by TLC and HPLC. Other P (III) intermediateswere not stable enough to monitor the coupling reaction and reactioncompletion was checked after the sulfurization was completed (scheme 1).P(V) species are more stable for dimers AA, GA, GG and GT. For TA dimer(5e), 1.3 equivalent of amidate (4c) was used for the coupling and theother four dimers (5a˜5d) required approximately 3 equivalent ofamidates (4a and 4b) (scheme 1). Amidate monomers 4a-4c are prepared byadapting methods described in U.S. Pat. No. 5,859,233.

The TBDMS protecting group at 5′-hydroxyl group was deprotected usingHF○pyridine in acetonitrile and the final phosphitylation was performedwith phosphitylating reagent in the presence of BMT andN-methylimidazole (NMI) to make the dimer thiophsophoroamidates, 7a to7e (Scheme 1). The final products (7) and three intermediates (3, 5, 6)were purified by column chromatography. The step and overall yields ofreactions with quantities of final amidates obtained are listed in Table3. Summary of analysis results for the five dimer amidates are shown inTable 4.

TABLE 3 Yields of Dimer Synthesis 5′-TBDMS- 5′-TBDMS- 5′-OH- OverallDimer 3′-Amino 3′-NH-Tr- 3′-NH-Tr Dimer yield (Quantity) NucleosideDimer Dimer amidate (%) TA 58% 91% 71% 51% 19.1% (2.9 g) AA 58% 82% 70%47% 15.6% (1.7 g) GA 58% 77% 60% 55% 14.7% (3.4 g) GG 58% 67% 57% 38%8.4% (1.9 g) GT 58% 99% 42% 38% 9.2% (1.8 g)

TABLE 4 Summary of Dimer Analysis Purity LCMS Amount Dimer by HPLC³¹P-NMR (Calc.) (g) TA 96.0% 148.281 (s), 148.193 (s), 1169.4 2.9 73.811(s), 73.723 (s), (1169.23) 72.981 (s), 72.592 (s) AA 95.8% 148.262 (m),74.034 (m), 1282.5 1.7 72.774 (d), 72.267 (d) (1282.35) GG 94.5% 148.156(m), 74.244 (s), 1268.5 (Na) 1.9 73.993 (s), 72.912 (s), (1246.32)72.761 (s) GT 95.3% 148.159 (m), 73.993 (s), 1151.4 1.8 73.811 (s),73.295 (s), (1151.22) 73.100 (s) GA 96.2% 148.168 (m), 148.011 (s),1264.5 3.4 74.175 (s), 73.942 (s), (1264.33) 73.170 (s), 72.906 (s)

Synthesis Procedure of Dimer Thiophosphoroamidates 1) Preparation of5′-TBDMS-3′-amino Nucleoside (for Adenosine and Guanosine)

a) Dissolve 5′-OH-3′-NH-Tr-2′-deoxynucleoside (1.0 eq) and imidazole(5.0 eq) in DMF and heat to 60° C.

b) Add TBDMSC1 (1.2 eq) to the heating solution then stir for 1 hr at60° C.

c) Add saturated aqueous NaHCO₃ solution to reaction mixture thenextract with ethyl acetate.

d) The organic layer is washed by saturated aqueous NaHCO₃ solution andbrine solution.

e) Add anhydrous Na₂SO₄ to the separated organic layer for drying thenfilter.

f) The filtrate is concentrated.

g) Add 80% aqueous acetic acid solution to the concentrated reactionmixture then stir for 1 hour at ambient temperature.

h) Remove the product solid by filtration then add saturated aqueousNaHCO₃ solution to the filtrate then extract by ethyl acetate fourtimes.

i) The organic layer is dried over anhydrous Na₂SO₄ then removed thesolid by filtration.

j) The filtrate is concentrated then purified by column chromatography(Eluent: Ethyl acetate:Methanol=9:1→5:1).

k) 5′-TBDMS-3′-amino-2′-daoxynucleoside is obtained as white solid.

2) Preparation of 5′-TBDMS-3′-amino Nucleoside (for Thymidine)

a) Dissolve 5′-OH-3′-amino-2′-deoxynucleoside (1.0 eq) and imidazole(5.0 eq) in DMF and heat up to 60° C.

b) Add TBDMSC1 (1.2 eq) to the heating solution then stirred for 1 hr at60° C.

c) Add saturated aqueous NaHCO₃ solution to reaction mixture thenextract with ethyl acetate four times.

d) Add anhydrous Na₂SO₄ to the organic layer for drying and filter.

e) The filtrate was concentrated.

f) The concentrated crude mixture is purified by column chromatography(Eluent: Ethyl acetate:Methanol=15:1→5:1).

g) 5′-TBDMS-3′-amino thymidine is obtained as a white solid.

3) Preparation of 5′-TBDMS-3′-NH-Tr Dimer

a) To remove the moisture, 5′-TBDMS-3′-amino nucleoside (1.0 eq) and BMT(benzylmercaptotetrazole, 1.0˜5.0 eq) are azeotroped by acetonitrilethree times then dissolved in DMF at ambient temperature under N₂atmosphere.

b) Add monomer amidate (3.0 eq) in DMF (using minimum amount to dissolvethe monomer amidate) to the reaction solution by drop wise then stir for1 hour at ambient temperature under nitrogen atmosphere. Monomer amidateis prepared according to methods described in U.S. Pat. No. 5,859,233.

c) Add xanthane hydride (2.0 eq) and pyridine (4.0 eq) to the reactionsolution then stir for 1 hour at ambient temperature under nitrogenatmosphere.

d) Add saturated aqueous NaHCO₃ solution to reaction mixture thenextract with ethyl acetate.

e) The aqueous layer is extracted with ethyl acetate.

f) The separated organic layers are combined and then washed bysaturated aqueous NaHCO₃ solution and brine solution.

g) Add anhydrous Na₂SO₄ to the organic layer for drying and filter, thenthe filtrate is concentrated.

h) The concentrated crude mixture is purified by column chromatography(Eluent: ethyl acetate:methanol=1.5:1→EA only).

i) 5′-TBDMS-3′-NH-Tr dimer is obtained as a pale yellow solid.

4) Preparation of 5′-OH-3′-NH-Tr Dimer

a) Dissolve 5′-TBDMS-3′-NH-Tr dimer (1.0 eq) in ACN (20 mL) undernitrogen atmosphere and then add HF— pyridine solution with stirring atambient temperature for 1.5 hours.

b) Add saturated aqueous NaHCO₃ solution to reaction mixture thenextract with ethyl acetate.

c) The separated organic layer is washed by saturated aqueous NaHCO₃solution and brine solution.

d) Add anhydrous Na₂SO₄ to the organic layer for drying and filteringthen the filtrate is concentrated.

e) The concentrated crude mixture is purified by column chromatography(Eluent: ethyl acetate, methanol, methylene chloride co-solvent)

f) 5′-OH-3′-NH-Tr dimer is obtained as a white solid.

5) Preparation of Dimer Phosphorothioamidate (Dimer Amidate)

A) To remove any moisture, 5′-Hydroxy-3′-NH-Tr dimer is azeotroped byacetonitrile three times then dissolved in ACN at ambient temperatureunder nitrogen atmosphere.

b) Add BMT (1.3 eq), NMI (N-Methyl imidazole, 0.3 eq) andphosphitylation reagent (2.0 eq) to the reaction solution then stir for1 hour at ambient temperature.

c) Add saturated aqueous NaHCO₃ solution to reaction mixture thenextract with ethyl acetate.

d) The separated organic layer is washed by brine solution.

e) Add anhydrous Na₂SO₄ to the organic layer for drying and filtering,then the filtrate is concentrated.

f) Dissolve concentrated reaction mixture in methylene chloride (10 mL)then add hexane to precipitate the solid.

g) Decant the upper solution layer to remove excess phosphitylationreagent. (Repeat decantation process 5 times).

h) The remaining solid is purified by column chromatography (Eluent:ethyl acetate, acetone, methylene chloride co-solvent)

i) Dimer is obtained as a white solid.

Imetelstat Synthesis Utilizing Dimer Amidates

Five dimer amidates were used in place of monomer amidates as thebuilding blocks for the synthesis of imetelstat and the results werecompared with the results obtained from the amidates of monomer. For thecoupling of the C nuceloside into imetelstat, the monomer building clockwas used as depicted in the sequence below. The synthesis was performedat a 140 μmole scale using an Akta Oligopilot 100.

(SEQ ID NO: 3) 5′R-TA GG GT TA GA C AA-NH₂ 3′

Dimer amidates were used as building blocks to make imetelstat. Usingthe reagents and synthesis parameters listed in Tables 5A and 5B, thefive dimer amidates (AA, TA, GG, GA, and GT) and one monomer amidate(C), as shown above, are coupled to make the imetelstat sequence onlow-loading CPG (PALM 0051, 64.6 μmol/g). The coupling time is 500 secand the 10 equivalency of the amidites were used. After the solid-phasesynthesis, the support is treated with ethanolic ammonium solution(NH₄OH:EtOH=3:1 (v/v)) at 65° C. for 15 hours. The crude product isisolated by evaporation of solvents and analyzed by UV spectroscopy andHPLC.

Table 5. Exemplary Synthesis Parameters (A) and Reagent Composition (B)for oligonucleotide Synthesis. ACN is acetonitrile. DCA isdichloroacetic acid. PADS is phenylacetyl disulfide. ETT is5-Ethylthio-1H-Tetrazole

TABLE 5 Exemplary Synthesis Parameters (A) and Reagent Composition (B)for oligonucleotide Synthesis. ACN is acetonitrile. DCA isdichloroacetic acid. PADS is phenylacetyl disulfide. ETT is5-Ethylthio-1H-Tetrazole A Step Reagenz Time RPM M 1 Wash 3.5 300 □ 2Gas 4.0 400 3 Debl 3.4 250 □ 4 Debl 2.0 250 □ 5 Dwait 60.0 6 Wash 12.0350 □ 7 Activ 3.0 250 8 COUPL 9 Wait 300.0 10 COUPL 11 Activ 1.3 150 12Wait 200.0 13 Wash 3.0 300 □ 14 Oxid 10.0 350 15 Wait 300.0 16 Oxid 10.0350 17 Wait 300.0 18 Wash 6.0 350 □ 19 CapA 3.0 200 20 CapB 1.5 150 21DWait 1.5 22 CapA 1.5 150 23 CapB 1.5 150 24 DWait 1.5 25 Wash 4.0 350 □B Reagent Name Composition Deblock 5% DCA in toluene Amidite 0.2M in ACNActivator 0.5M ETT in ACN Thiolation 0.2M PADS in ACN:LTD = 1:1 Cap A20% NMI on ACN Cap B IBUA:LTD:ACN = 1:1:8 DEA 20% DEA in ACN

Using an Akta Oligopilot 100, synthesis runs on a 140 μmole scale wereconducted using the monomer block method and the dimer block blockmethod. The synthesis conditions for the synthesis runs were similar tothose listed in Table 5A-B.

TABLE 6 Synthetic Parameters for 140 μmole scale Synthesis (AKTAOligopilot 100) Imetelstat Imetelstat Synthesis using Synthesis usingParameters Monomers Dimers Deblock CT (min) 3 min (2nd 6 min) 3 min (5%DCA in toluene) CV 11.2 CV   Linear flow (cm/hr) 450 cm/hr CouplingAmidate 0.1M, 2.5 eq 0.1M, 2.5 eq (last 2: 3.0 eq) (last AA: 3.0 eq)Activator 0.5M ETT (Amidate:Activator, 4:6) 1st Coupling double couplingCT for Flow through 1.8 min  (min) CT for Recycle (min) 1.8 min (1st: 4min)   Thiolation CT (min) 5.27 min  (0.1M PADS CV 3.5 CV  in AN:LTD =9:1) Linear flow (cm/hr)  80 cm/hr Capping CT (min) 1 min (1st: 2 min)(Cap A: 20% NMI in AN, CV 1 CV (1st: 2 CV) CapB: IBUA:LTD:AN = 1:1:8)Linear flow (cm/hr) 120 cm/hr DEA CT (min) 10 min  (20% DEA in AN) CV4.3 CV  Linear flow (cm/hr)  52 cm/hr

Analysis of oligonucleotides by HPLC-MS showed that the FLP (full lengthproduct) purity was improved significantly when the five dimer blockswere used for synthesis, giving 72% purity by HPLC as summarized inTables 7 and 8. The crude oligo prepared using the monomer blocks showedonly 45% FLP purity. Further, the total GD (optical density) wasincreased by more than double from 5,299 to 11,623 affording the crudeyield of 3.34 g/mmol. The (N−1) product level and the PG content weredecreased to 2.4% from 11.2% and to 5% from 20%, respectively.

An advantage of using dimer blocks includes that the production time isshortened and the amounts of solvents used during the solid-phasesynthesis are reduced.

TABLE 7 Analysis Result for 140 μmole Scale Synthesis ImetelstatImetelstat Synthesis using Synthesis using Attributes Monomer AmidateDimer Amidate HPLC FLP 44.4% 74.0% Post-peak1 11.0% 2.4% (N-1) productUV TOD 5299 11623 Weight (mg) 213 mg 468 mg g/mmol 1.52 3.34 LC/MS FLP70.3% 71.9% n-117 3.3% 16.4% n-133 6.5% 6.7% n-16 19.9% 5.0%

The synthesis of five dimer amidates was completed successfully with theyields of 9% to 19% from 5′-hydroxy-3′-amino nucleoside or5′-hydroxy-3′-tritylamino nucleoside giving 1.7 gram to 3.4 gram.Optimization of reaction conditions for each step was not studiedextensively. The dimers block syntheses of imetelstat were conducted ona 140 μmol scale and the results were compared with the data obtainedfrom synthesis using monomer amidates. The dimer blocks strategy forpreparation of imetelstat was shown to provide substantial improvementsbecause the purity and yield were improved significantly, e.g., on a 140μmol scale (HPLC Purity: dimer 74.0% (FIG. 8), monomer 44.4% (FIG. 7),Crude yield by TOD (total optical density): dimer 468 mg, monomer 213mg). In addition a lower amount of npo linkage was generated since therewere fewer coupling steps in the synthesis using dimers.

Coupling efficiency for the dimer (140 μmole scale Synthesis) shows thatthe dimer synthesis had 96% coupling efficiency whereas the monomersynthesis is at 94%. Since there were only seven coupling for the dimerthe FLP for dimer was at 71.6% which is close to the theoreticallycalculated Full Length Product at 72% and the monomer with 13 couplingsreported a FLP of 45.6% vs the theoretically predicted at 44%.

TABLE 8 Analysis of Results for 140 μmole Scale Synthesis % area % areaProducts of Retention monomer Products of Retention dimer monomersynthesis time (min) synthesis dimer synthesis time (min) synthesistarget 38.2 44.4 target 37.9 74.0 Post Peak 1 39.8 11.0 Post Peak 1 39.82.5 N-1 (N-G) N-1 (N-C) Post Peak 2 41.2 6.3 Post Peak 2 41.3 3.9 N-2 +iBu, N-2, N-2 + iBu, N-2, N-G + Phenylacetyl N-G + Phenylacetyl PostPeak 3 42.9 6.9 Post Peak 3 42.4 5.1 N-2 + Phenylacetyl, N-2 +Phenylacetyl, N-3 (N-A-A-C) N-3 (N-A-A-C) Post Peak 4 44.7 6.0 Post Peak4 44.5 1.6 N-3 + Phenylacetyl N-3 + Phenylacetyl Total non-target39.8-54.7 49.5 Total non-target 39.7-53.1 19.8 oligonucleotidesoligonucleotides “+Phenylacetyl” denotes a product derived from reactionwith an oxidation reagent

Imetelstat synthesis utilizing fewer coupling steps provides for bothFull Length Product Purity and Yield that are substantially higher.Resolution of impurities provides easier purification of imetelstatwhere there are less amounts of minor products closely running near themain peak in HPLC to produce compositions having higher purity ofimetelstat. This improvement is desirable for lower cost of goods formanufacture of imetelstat sodium, e.g., the cost of goods can be 30-40%less when implemented at manufacturing scale.

85 g of TBAG was prepared from 300 g of APG2 according to the methodsdescribed herein via the steps shown in Scheme 2.

430 g of TBAPA1 was obtained from 800 g of the crude APA1 (purity: 46%)according to the methods described herein via the steps shown in Scheme3.

TA dimer amidate (5) has been prepared according to the methodsdescribed herein via the steps shown in Scheme 4 at scales of synthesisfrom 100 mg to 1 g.

TABLE 9 Coupling and Sulfurization during Dimer Amidate synthesisStarting Material Solvent type Reaction Pdt. Yield Entry Quantity Mol.Eq. of reagents and Amount time/temp. Weight Analysis 1 100 mg ETT (1.0eq), Acetonitrile RT for 300 mg LCMS Xantane hydride (2.0eq), (5.0 mL)3 + 2 h. (crude) Pyridine (1.5 mL) 2 100 mg 0.4M ETT (2.0 mL), neat RTfor 350 mg LCMS Xantane hydride (1.2eq), 3 + 2 h. (crude) Pyridine (2.0mL)

A variety of nucleoside monomers were prepared according to the methodsdescribed herein which find use in the preparation of the dimercompounds.

While the present invention has been described with reference to thespecific embodiments thereof, it should be understood by those skilledin the art that various changes may be made and equivalents may besubstituted without departing from the true spirit and scope of theinvention. In addition, many modifications may be made to adapt aparticular situation, material, composition of matter, process, processstep or steps, to the objective, spirit and scope of the presentinvention. All such modifications are intended to be within the scope ofthe claims appended hereto.

Embodiments

The present disclosure provides a composition having less than 1 part in4 by weight of a (N−1) product relative to a compound or a salt thereof,where the compound includes a polynucleotide having a sequence of 10 ormore nucleoside subunits and at least two of the nucleoside subunits arejoined by a N3′→P5′ phosphoramidate inter-subunit linkage. In someembodiments of the composition, the N3′→P5′ phosphoramidateinter-subunit linkage is a N3′→P5′ thiophosphoramidate inter-subunitlinkage having the structure: 3′-NH—P(S)(OR) O-5′ where R is selectedfrom the group consisting of hydrogen, an alkyl, a substituted alkyl, anaryl, a substituted aryl and a phosphate protecting group, or a saltthereof.

In some embodiments of the composition, the compound includes apolynucleotide having a sequence of 10 or more nucleoside subunitscomplementary to the RNA component of human telomerase. In someembodiments of the composition, the polynucleotide includes a sequencecomprising 13 or more nucleoside subunits complementary to the RNAcomponent of human telomerase. In some embodiments of the composition,the polynucleotide includes between 3 and 50 contiguous nucleosidesubunits complementary to the RNA component of human telomerase. In someembodiments of the composition, the nucleoside subunits complementary tothe RNA component of human telomerase are all joined by N3′→P5′phosphoramidate inter-subunit linkages. In some embodiments of thecomposition, the polynucleotide includes a sequence selected from thegroup consisting of: GTTAGGGTTAG (SEQ ID NO:4), TAGGGTTAGACAA (SEQ IDNO:3) and CAGTTAGGGTTAG (SEQ ID NO:5). In some embodiments of thecomposition, the polynucleotide includes a 3′amino or a 3′-hydroxylterminal group.

In some embodiments of the composition, the compound has the structure:

or a salt thereof; where “nps” represents a thiophosphoramidate linkage—NH—P(═O)(SH) O—, connecting the 3′-carbon of one nucleoside to the5′-carbon of the adjacent nucleoside. In some embodiments of thecomposition, the salt is a pharmaceutically acceptable salt.

In some embodiments of the composition, the compound has the structure:

wherein each M^(x+) is independently hydrogen or a counterion of a salt,each x is independently 1, 2 or 3 and n is an integer from 5 to 13. Incertain instances, M^(x+) is hydrogen.

In some embodiments of the composition, the compound has the structure:

In some embodiments, the composition has less than 1 part in 6 by weightof a (N−1) product relative to the compound. In some embodiments, thecomposition has less than 1 part in 10 by weight of a (N−1) productrelative to the compound. In some embodiments, the composition has lessthan 1 part in 20 by weight of a (N−1) product relative to the compound.In some embodiments, the composition has less that 1 part in 4 by weightof any (N−x) product relative to the compound. In some embodiments, thecomposition has less that 40 part in 100 by total weight of (N−x)polynucleotide-containing products relative to the compound. In someembodiments, the composition has the following profile of (N−x)polynucleotide-containing products: less that 1 part in 4 by weight of a(N−1) product relative to the compound; at least 10 parts in 100 byweight of (N−2) and (N−3) products relative to the compound.

The present disclosure provides a compound active pharmaceuticalingredient having less than 11% by weight of a (N−1) product, where thecompound or a pharmaceutically acceptable salt thereof includes apolynucleotide having a sequence of 10 or more nucleoside subunitscomplementary to the RNA component of human telomerase, where at leasttwo of the nucleoside subunits are joined by a N3′→P5′ phosphoramidateinter-subunit linkage.

In some embodiments of the compound active pharmaceutical ingredient,the nucleoside subunits complementary to the RNA component of humantelomerase are all joined by N3′→P5′ thiophosphoramidate inter-subunitlinkages. In some embodiments of the compound active pharmaceuticalingredient, the N3′→P5′ phosphoramidate inter-subunit linkage is aN3′→P5′ thiophosphoramidate inter-subunit linkage having the structure:3′-NH—P(S)(OR) O-5′ where R is selected from the group consisting ofhydrogen, an alkyl, a substituted alkyl, an aryl, a substituted aryl anda phosphate protecting group, or a pharmaceutically acceptable saltthereof.

In some embodiments of the compound active pharmaceutical ingredient,the polynucleotide includes between 10 and 50 contiguous nucleosidesubunits complementary to the RNA component of human telomerase. In someembodiments of the compound active pharmaceutical ingredient, thepolynucleotide includes a sequence selected from the group consistingof: GTTAGGGTTAG (SEQ ID NO:4); TAGGGTTAGACAA (SEQ ID NO:3); andCAGTTAGGGTTAG (SEQ ID NO:5). In some embodiments of the compound activepharmaceutical ingredient, the polynucleotide includes a 3′amino or a3′-hydroxyl terminal group.

In some embodiments of the compound active pharmaceutical ingredient,the compound has the structure:

or a pharmaceutically acceptable salt thereof; where “nps” represents athiophosphoramidate linkage —NH—P(═O)(SH)—O—, connecting the 3′-carbonof one nucleoside to the 5′-carbon of the adjacent nucleoside.

In some embodiments of the compound active pharmaceutical ingredient,the compound has the structure:

where each M^(x+) is independently hydrogen or a counterion of apharmaceutically acceptable salt, each x is independently 1, 2 or 3 andn is an integer from 5 to 13. In certain instances, M^(x+) is hydrogen.

In some embodiments of the compound active pharmaceutical ingredient,the compound has the structure:

In some embodiments, the compound active pharmaceutical ingredient hasless that 9% by weight of the (N−1) product. In some embodiments, thecompound active pharmaceutical ingredient has less that 5% by weight ofthe (N−1) product. In some embodiments, the compound activepharmaceutical ingredient has less that 11% of any (N−x) product. Insome embodiments, the compound active pharmaceutical ingredient has lessthat 45% by weight in total of (N−x) polynucleotide-containing products.In some embodiments, the compound active pharmaceutical ingredient hasthe following profile of (N−x) polynucleotide-containing products: lessthat 5% by weight of a (N−1) product; and at least 10% by weight of(N−2) and (N−3) products.

Also provided is a pharmaceutical composition including a composition(e.g., of any one of the embodiments described herein) formulated in apharmaceutically acceptable excipient. Also provided is a pharmaceuticalcomposition including a compound active pharmaceutical ingredient (e.g.,of any one of the embodiments described herein) formulated in apharmaceutically acceptable excipient.

The present disclosure provides a method of synthesizing apolynucleotide. In some embodiments, the method includes the steps of:(a) deprotecting the protected 3′ amino group of a terminal nucleosideattached to a solid phase support, said deprotecting forming a free 3′amino group; (b) contacting the free 3′ amino group with a 3′-protectedamino-dinucleotide phosphoramidate-5′-phosphoramidite dimer in thepresence of a nucleophilic catalyst to form an internucleoside N3′→P5′phosphoramidite linkage; and (c) oxidizing the linkage.

In some embodiments, the method further includes: (a) deprotecting theprotected 3′ amino group of a terminal nucleoside attached to a solidphase support, said deprotecting forming a free 3′ amino group; (b)contacting the free 3′ amino group with a 3′-protectedaminonucleoside-5′-phosphoramidite monomer in the presence of anucleophilic catalyst to form an internucleoside N3′→P5′ phosphoramiditelinkage; and (c) oxidizing the linkage. In some embodiments of themethod, the oxidizing the linkage includes sulfurization to produce athiophosphoramidate linkage. In some embodiments of the method, theoxidizing the linkage produces an oxophosphoramidate linkage.

In some embodiments of the method, the 3′-protected amino-dinucleotidephosphoramidate-5′-phosphoramidite dimer has the formula:

wherein X is O or S and B¹ and B² are each independently a purine, aprotected purine, a pyrimidine or a protected pyrimidine, or an analogthereof. In some embodiments of the method, the B¹ and B² are eachindependently selected from protected adenine, protected cytosine,protected guanine, thymine and uracil. In some embodiments of themethod, the B¹ and B² are each independently selected from A(Bz),A(DMF), C(Bz), G(isobutyryl), T and U. In some embodiments of themethod, X is S.

In some embodiments of the method, the polynucleotide is of the formula:

where: each B is independently a purine, a protected purine, apyrimidine or a protected pyrimidine, or an analog thereof; each X isindependently oxygen or sulfur; each R³ is hydrogen, fluoro, orhydroxyl, an alkoxy, a substituted alkoxy or a protected hydroxyl; L isan optional linker; Z is H, a lipid, a support, a carrier, anoligonucleotide, a PEG, a polypeptide, a detectable label, or a tag; R⁶is amino, hydroxyl, a protected amino, a protected hydroxy, —O-L-Z or—NH-L-Z; R is hydrogen, an alkyl, a substituted alkyl, an aryl, asubstituted aryl, or a phosphate protecting group; and n is an integerof 1 to 1000; or a salt thereof; and the method comprises the steps of:(a) deprotecting a protected 3′ amino group of a terminal nucleosideattached to a solid phase support, said deprotecting forming a free 3′amino group; (b) reacting the free 3′ amino group with either: (i) a3′-protected amino-dinucleotide phosphoramidate-5′-phosphoramiditedimer; or(ii) a 3′-protected aminonucleoside-5′-phosphoramidite monomer; in thepresence of a nucleophilic catalyst to form an internucleoside N3′→P5′phosphoramidite linkage; (c) oxidizing the linkage; and (d) repeatingsteps (a) through (c) until the polynucleotide is synthesized, whereinthe repeating steps (a) through (c) comprises performing step (b)(i) atleast once.

In some embodiments of the method, the oxidizing the linkage comprisessulfurization to produce a thiophosphoramidate linkage. In someembodiments of the method, the oxidizing the linkage produces anoxophosphoramidate linkage. In some embodiments of the method, thepolynucleotide comprises a sequence of nucleoside subunits complementaryto the RNA component of human telomerase, and wherein at least two ofthe nucleoside subunits are joined by a N3′→P5′ phosphoramidateinter-subunit linkage. In some embodiments of the method, the N3′→P5′phosphoramidate inter-subunit linkage is a N3′→P5′ thiophosphoramidateinter-subunit linkage having the structure: 3′-NH—P(S)(OR)—O-5′ where Ris selected from the group consisting of hydrogen, an alkyl, asubstituted alkyl, an aryl, a substituted aryl and a phosphateprotecting group, or a salt thereof.

In some embodiments of the method, the polynucleotide includes thesequence TAGGGTTAGACAA. In some embodiments of the method, all of theinternucleotide inter-subunit linkages of the TAGGGTTAGACAA sequence areN3′→P5′ phosphoramidate inter-subunit linkages. In some embodiments ofthe method, polynucleotide has the structure:

or a salt thereof; where “nps” represents a thiophosphoramidate linkage—NH—P(═O)(SH)—O—, connecting the 3′-carbon of one nucleoside to the5′-carbon of the adjacent nucleoside.

In some embodiments of the method, the polynucleotide has the structure:

wherein each M^(x+) is independently hydrogen or a counterion of apharmaceutically acceptable salt, each x is independently 1, 2 or 3 andn is an integer from 5 to 13. In certain instances, M^(x+) is hydrogen.

In some embodiments of the method, the polynucleotide has the structure:

In some embodiments of the method, the C11 nucleotide residue of theTAGGGTTAGACAA sequence derives from a 3′-protectedaminonucleoside-5′-phosphoramidite monomer. In some embodiments, themethod includes sequential coupling of the following 3′-protectedamino-dinucleotide thiophosphoramidate-5′-phosphoramidite dimers TA, GG,GT, TA, GA and AA and 3′-protected aminonucleoside-5′-phosphoramiditemonomer C to the solid phase support. In some embodiments of the method,the 3′-protected amino-dinucleotide phosphoramidite-5′-phosphoramiditedimer is described by the formula X¹X² wherein X¹ and X² areindependently selected from protected adenine, protected cytosine,protected guanine, thymine and uracil. In some embodiments of themethod, the 3′-protected aminonucleoside-5′-phosphoramidite dimer isselected from protected adenine, protected cytosine, protected guanine,thymine and uracil.

The present disclosure provides a dinucleotide thiophosphoramidatecompound described by Formula (II):

wherein: B¹ and B² are each independently a purine, a protected purine,a pyrimidine or a protected pyrimidine, or an analog thereof; R¹¹ ishydrogen, a protecting group or a phosphoramidite group; and R¹² and R¹³are each independently hydrogen or a protecting group; or a saltthereof.

In some embodiments of the compound, B¹ and B² are each independentlyselected from protected adenine, protected cytosine, protected guanine,thymine and uracil. In some embodiments of the compound, B¹ and B² areeach independently selected from A(Bz), A(DMF), C(Bz), G(isobutyryl), Tand U. In some embodiments of the compound, R¹¹ is a 5′-phosphoramidite;R¹² is a protecting group and R¹³ is a protecting group. In someembodiments of the compound, B¹ is A(Bz) or A(DMF) and B² is A(Bz) orA(DMF). In some embodiments of the compound, B¹ is A(Bz) or A(DMF) andB² is C(Bz). In some embodiments of the compound, B¹ is A(Bz) or A(DMF)and B² is G(isobutyryl). In some embodiments of the compound, B¹ isA(Bz) or A(DMF) and B² is T. In some embodiments of the compound, B¹ isA(Bz) or A(DMF) and B² is U. In some embodiments of the compound, B¹ isC(Bz) and B² is A(Bz) or A(DMF). In some embodiments of the compound, B¹is C(Bz) and B² is C(Bz). In some embodiments of the compound, B¹ isC(Bz) and B² is G(isobutyryl). In some embodiments of the compound, B¹is C(Bz) and B² is T. In some embodiments of the compound, B¹ is C(Bz)and B² is U. In some embodiments of the compound, B¹ is G(isobutyryl)and B² is A(Bz) or A(DMF). In some embodiments of the compound, B1 isG(isobutyryl) and B² is C(Bz). In some embodiments of the compound, B¹is G(isobutyryl) and B² is G(isobutyryl). In some embodiments of thecompound, B1 is G(isobutyryl) and B² is T. In some embodiments of thecompound, B¹ is G(isobutyryl) and B² is U. In some embodiments of thecompound, B¹ is T or U and B² is A(Bz) or A(DMF). In some embodiments ofthe compound, B is T or U and B² is C(Bz). In some embodiments of thecompound, B¹ is T or U and B² is G(isobutyryl). In some embodiments ofthe compound, B¹ is T or U and B² is T. In some embodiments of thecompound, B¹ is T or U and B² is U.

All possible combinations of the above-indicated embodiments areconsidered to be embraced within the scope of this invention.

1.-55. (canceled)
 56. A dinucleotide thiophosphoramidate compounddescribed by Formula (II):

wherein: B¹ and B² are each independently a purine, a protected purine,a pyrimidine or a protected pyrimidine, or an analog thereof; R¹¹ is aphosphoramidite group; and R¹² and R¹³ are each independently aprotecting group; or a salt thereof.
 57. The compound of claim 56,wherein B¹ and B² are each independently selected from protectedadenine, protected cytosine, protected guanine, thymine and uracil. 58.The compound of claim 57, wherein B¹ and B² are each independentlyselected from A(Bz), A(DMF), C(Bz), G(isobutyryl), T and U. 59.(canceled)
 60. The compound of claim 58, wherein B¹ is A(Bz) or A(DMF)and B² is A(Bz) or A(DMF).
 61. The compound of claim 58, wherein B¹ isA(Bz) or A(DMF) and B² is C(Bz).
 62. The compound of claim 58, whereinB¹ is A(Bz) or A(DMF) and B² is G(isobutyryl).
 63. The compound of claim58, wherein B¹ is A(Bz) or A(DMF) and B² is T.
 64. The compound of claim58, wherein B¹ is A(Bz) or A(DMF) and B² is U.
 65. The compound of claim58, wherein B¹ is C(Bz) and B² is A(Bz) or A(DMF).
 66. The compound ofclaim 58, wherein B¹ is C(Bz) and B² is C(Bz).
 67. The compound of claim58, wherein B¹ is C(Bz) and B² is G(isobutyryl).
 68. The compound ofclaim 58, wherein B¹ is C(Bz) and B² is T.
 69. The compound of claim 58,wherein B¹ is C(Bz) and B² is U.
 70. The compound of claim 58, whereinB¹ is G(isobutyryl) and B² is A(Bz) or A(DMF).
 71. The compound of claim58, wherein B¹ is G(isobutyryl) and B² is C(Bz).
 72. The compound ofclaim 58, wherein B¹ is G(isobutyryl) and B² is G(isobutyryl).
 73. Thecompound of claim 58, wherein B¹ is G(isobutyryl) and B² is T.
 74. Thecompound of claim 58, wherein B¹ is G(isobutyryl) and B² is U.
 75. Thecompound of claim 58, wherein B¹ is T or U and B² is A(Bz) or A(DMF).76. The compound of claim 58, wherein B¹ is T or U and B² is C(Bz). 77.The compound of claim 58, wherein B¹ is T or U and B² is G(isobutyryl).78. The compound of claim 58, wherein B¹ is T or U and B² is T.
 79. Thecompound of claim 58, wherein B¹ is T or U and B² is U.